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This page was generated on 2024-04-18 11:32:07 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 196/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_18
git_last_commit: 664af9c
git_last_commit_date: 2023-10-24 11:36:37 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbChebi on kjohnson1


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

raw results

Summary

Package: biodbChebi
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-04-17 07:09:46 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 07:11:08 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 81.8 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/biodbChebi.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.8.0’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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/4.3-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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 [2024-04-17 07:10:40.096][biodb::testContext]
biodb.INFO [2024-04-17 07:10:40.101][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:10:40.102][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-04-17 07:10:40.103][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:10:40.104][biodb::testContext]
biodb.INFO [2024-04-17 07:10:40.115][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:10:40.117][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-17 07:10:40.129][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:40.130][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-17 07:10:40.131][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-17 07:10:40.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.135][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-17 07:10:40.155][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-17 07:10:40.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.158][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[2024-04-17 07:10:40.159][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-17 07:10:40.160][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-17 07:10:40.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.163][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-17 07:10:40.164][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-17 07:10:40.165][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-17 07:10:40.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.168][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.DEBUG[2024-04-17 07:10:40.169][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-17 07:10:40.170][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-17 07:10:40.171][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-17 07:10:40.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.174][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-17 07:10:40.175][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-17 07:10:40.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.177][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[2024-04-17 07:10:40.178][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-17 07:10:40.179][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-17 07:10:40.180][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-17 07:10:40.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.184][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-17 07:10:40.185][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-17 07:10:40.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.188][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-17 07:10:40.189][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-17 07:10:40.190][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-17 07:10:40.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.193][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:10:40.194][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-17 07:10:40.195][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-17 07:10:40.196][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-17 07:10:40.197][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-17 07:10:40.198][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-17 07:10:40.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.202][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-17 07:10:40.203][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-17 07:10:40.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.206][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-17 07:10:40.207][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-17 07:10:40.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.209][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[2024-04-17 07:10:40.210][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-17 07:10:40.211][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-17 07:10:40.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.215][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-17 07:10:40.215][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-17 07:10:40.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.219][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-17 07:10:40.220][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-17 07:10:40.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.223][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:10:40.224][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-17 07:10:40.240][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-17 07:10:40.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.244][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.DEBUG[2024-04-17 07:10:40.245][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-17 07:10:40.246][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-17 07:10:40.247][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-17 07:10:40.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.256][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-17 07:10:40.296][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.322][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-17 07:10:40.323][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:40.325][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.326][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.326][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.327][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.328][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:10:40.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:40.330][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.331][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-17 07:10:40.331][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:40.332][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.333][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.334][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:40.334][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:40.334][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:40.334][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:10:40.334][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:10:40.335][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:40.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.337][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:40.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.340][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.341][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.342][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:40.343][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:40.343][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.344][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.345][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-17 07:10:40.347][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.348][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:10:40.349][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.349][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:40.350][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.351][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.352][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.352][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.353][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:10:40.354][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:40.355][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.356][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-17 07:10:40.356][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:40.357][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.358][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.359][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:40.359][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:40.359][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:40.359][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:10:40.359][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:10:40.360][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:40.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.364][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.365][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:40.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.368][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.369][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.369][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:40.370][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:40.371][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.372][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.373][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-17 07:10:40.374][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.375][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-17 07:10:40.376][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.377][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:40.378][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.379][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.379][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.380][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.381][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:10:40.382][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:40.383][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.383][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-17 07:10:40.384][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:40.385][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.386][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.386][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.387][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:40.388][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.390][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:40.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.392][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.393][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.393][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:40.394][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:40.395][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.396][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.397][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-17 07:10:40.398][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.399][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:10:40.400][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.401][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:40.402][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.403][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.403][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.404][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.405][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:10:40.408][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:40.410][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.411][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-17 07:10:40.412][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:40.413][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.414][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.414][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.415][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:40.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.418][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:40.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.420][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.421][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.421][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:40.422][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:40.423][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.424][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:40.431][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:40.432][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.444][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[2024-04-17 07:10:40.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.455][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.DEBUG[2024-04-17 07:10:40.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.494][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[2024-04-17 07:10:40.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.497][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[2024-04-17 07:10:40.498][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-17 07:10:40.505][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-17 07:10:40.507][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-17 07:10:40.509][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-17 07:10:40.510][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:10:40.512][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-17 07:10:40.513][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-17 07:10:40.514][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-17 07:10:40.515][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-17 07:10:40.516][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-17 07:10:40.518][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:10:40.519][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-17 07:10:40.520][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-17 07:10:40.521][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-17 07:10:40.522][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-17 07:10:40.523][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:10:40.525][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-17 07:10:40.526][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-17 07:10:40.527][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:10:40.535][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-17 07:10:40.537][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-17 07:10:40.538][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-17 07:10:40.540][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-17 07:10:40.542][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-17 07:10:40.544][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-17 07:10:40.546][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-17 07:10:40.548][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-17 07:10:40.550][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-17 07:10:40.552][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-17 07:10:40.553][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-17 07:10:40.555][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-17 07:10:40.556][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-17 07:10:40.557][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-17 07:10:40.558][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-17 07:10:40.559][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-17 07:10:40.561][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-17 07:10:40.562][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-17 07:10:40.563][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-17 07:10:40.564][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-17 07:10:40.565][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-17 07:10:40.566][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-17 07:10:40.568][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-17 07:10:40.569][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-17 07:10:40.570][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-17 07:10:40.571][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-17 07:10:40.572][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-17 07:10:40.574][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-17 07:10:40.575][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-17 07:10:40.577][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-17 07:10:40.579][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-17 07:10:40.581][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-17 07:10:40.583][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-17 07:10:40.584][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-17 07:10:40.585][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-17 07:10:40.586][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-17 07:10:40.588][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-17 07:10:40.590][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-17 07:10:40.591][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-17 07:10:40.592][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-17 07:10:40.593][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-17 07:10:40.594][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-17 07:10:40.596][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-17 07:10:40.597][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-17 07:10:40.598][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-17 07:10:40.599][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-17 07:10:40.600][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-17 07:10:40.601][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:10:40.603][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:10:40.605][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-17 07:10:40.607][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-17 07:10:40.608][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-17 07:10:40.610][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-17 07:10:40.611][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-17 07:10:40.612][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-17 07:10:40.614][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-17 07:10:40.615][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-17 07:10:40.616][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-17 07:10:40.617][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-17 07:10:40.618][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-17 07:10:40.619][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-17 07:10:40.621][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-17 07:10:40.622][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-17 07:10:40.623][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-17 07:10:40.629][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-17 07:10:40.631][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:10:40.636][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:40.638][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.640][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.658][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[2024-04-17 07:10:40.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.700][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[2024-04-17 07:10:40.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.706][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[2024-04-17 07:10:40.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:40.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.727][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[2024-04-17 07:10:40.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.732][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[2024-04-17 07:10:40.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:40.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.739][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[2024-04-17 07:10:40.742][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-04-17 07:10:40.751][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-04-17 07:10:40.753][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.754][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.755][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.755][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:40.756][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.757][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.758][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.758][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-04-17 07:10:40.759][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-04-17 07:10:40.760][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:40.768][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.769][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-04-17 07:10:40.771][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-04-17 07:10:40.772][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-04-17 07:10:40.773][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:40.774][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:40.774][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:40.774][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:40.775][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-17 07:10:40.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.777][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:40.778][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:40.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:40.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:40.780][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:40.780][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-04-17 07:10:40.781][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:40.782][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:40.783][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:40.784][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-04-17 07:10:40.784][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-04-17 07:10:40.790][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:10:40.792][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:10:40.793][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-04-17 07:10:40.794][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:10:40.795][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:10:40.797][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:10:40.834][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-04-17 07:10:40.836][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-04-17 07:10:40.842][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-04-17 07:10:40.848][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-04-17 07:10:40.854][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-17 07:10:40.856][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-17 07:10:40.858][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-04-17 07:10:40.862][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-04-17 07:10:40.880][biodb::testThat]
biodb.INFO [2024-04-17 07:10:40.881][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-04-17 07:10:40.882][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:40.883][biodb::testThat]
biodb.TRACE[2024-04-17 07:10:40.888][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-04-17 07:10:40.890][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:40.895][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:40.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:40.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:40.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:40.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:40.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:40.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:40.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:40.945][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:40.946][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:40.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:40.948][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:40.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:40.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:40.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:40.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:40.966][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:40.967][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:40.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:40.968][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:40.994][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:40.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:40.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:40.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:40.998][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:40.999][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.001][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.002][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:41.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.006][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.008][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.012][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.013][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.014][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.019][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.020][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.021][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.022][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.025][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:41.026][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.028][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.029][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:41.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.032][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.033][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.034][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.039][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.040][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.041][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.046][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:41.046][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.048][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.049][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:41.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.052][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.053][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.055][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.056][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:41.137][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-04-17 07:10:41.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:10:41.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:10:41.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:10:41.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:10:41.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-17 07:10:41.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-17 07:10:41.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.191][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-17 07:10:41.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-17 07:10:41.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.304][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.305][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.307][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.324][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.325][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.338][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.339][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.341][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.352][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:41.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.357][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:41.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.362][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:41.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.366][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:41.368][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.370][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.371][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:41.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.393][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.393][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.394][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.417][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.418][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.420][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.431][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:41.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:41.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.436][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:41.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:41.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.438][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:41.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:41.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.440][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:41.440][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:41.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.441][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.441][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:41.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:41.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.488][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.493][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.496][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.498][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.498][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.499][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.500][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.505][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.507][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.508][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.510][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.510][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.511][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.511][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.519][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.521][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.522][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.523][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.523][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.523][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.547][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.548][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.549][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.569][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.570][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.570][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.581][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.584][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.590][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:41.591][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:41.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.593][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.598][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:41.599][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.601][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.606][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.607][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.609][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.614][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.615][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.616][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.621][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.623][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.625][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.630][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.631][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.633][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.637][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.638][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.640][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.645][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.646][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.647][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.652][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.660][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.662][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.667][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.668][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.670][ef$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:41.678][biodb::testThat]
biodb.INFO [2024-04-17 07:10:41.679][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-17 07:10:41.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:41.680][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:41.695][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-04-17 07:10:41.700][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:41.703][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-04-17 07:10:41.703][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:41.704][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-04-17 07:10:41.704][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:41.716][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:41.718][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:41.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:41.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:41.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:41.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:41.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:41.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:41.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:41.728][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.729][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.739][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:41.740][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:41.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.741][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.742][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:41.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:41.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.744][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:41.745][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.745][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.746][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:41.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:41.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.749][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.749][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.750][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:41.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:41.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.752][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.752][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.753][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:41.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.755][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.755][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.756][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.757][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:41.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.758][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:41.759][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.759][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.760][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:41.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.762][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.762][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.763][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.765][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.765][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.766][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.768][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:41.768][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.769][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.770][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:41.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:41.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.771][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.771][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.772][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.774][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:41.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:41.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:41.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:41.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:41.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:41.797][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-04-17 07:10:41.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-17 07:10:41.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-17 07:10:41.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-17 07:10:41.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-17 07:10:41.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-17 07:10:41.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-17 07:10:41.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:41.806][biodb::testThat]
biodb.INFO [2024-04-17 07:10:41.807][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-17 07:10:41.807][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:41.808][biodb::testThat]
biodb.TRACE[2024-04-17 07:10:41.809][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.810][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.810][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:41.811][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-04-17 07:10:41.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:41.841][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-04-17 07:10:41.847][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-04-17 07:10:41.867][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:41.882][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-04-17 07:10:41.884][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:41.885][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-04-17 07:10:41.910][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[2024-04-17 07:10:41.914][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:41.915][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-17 07:10:41.917][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:41.918][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-17 07:10:41.919][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-04-17 07:10:41.931][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.932][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:41.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.932][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.933][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.933][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:41.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.936][ef$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:41.942][biodb::testThat]
biodb.INFO [2024-04-17 07:10:41.943][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-04-17 07:10:41.944][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:41.944][biodb::testThat]
biodb.TRACE[2024-04-17 07:10:41.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:41.981][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:41.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:41.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:41.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:42.039][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[2024-04-17 07:10:42.043][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:42.044][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-17 07:10:42.045][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:42.047][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-04-17 07:10:42.064][biodb::testThat]
biodb.INFO [2024-04-17 07:10:42.065][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-04-17 07:10:42.066][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:42.066][biodb::testThat]
biodb.TRACE[2024-04-17 07:10:42.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:42.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:42.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:42.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:42.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:42.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:42.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:42.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:42.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:42.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:42.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:42.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:42.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.104][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:10:42.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:10:42.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.107][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:10:42.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:10:42.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.111][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-17 07:10:42.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-17 07:10:42.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.115][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-17 07:10:42.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-17 07:10:42.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:42.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:42.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:42.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:42.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:42.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:42.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:42.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:42.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:42.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:42.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:42.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.149][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:10:42.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:10:42.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:10:42.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:10:42.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-17 07:10:42.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-17 07:10:42.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:42.155][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-17 07:10:42.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-17 07:10:42.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:42.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:42.161][biodb::testThat]
biodb.INFO [2024-04-17 07:10:42.162][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-17 07:10:42.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:42.163][biodb::testThat]
biodb.INFO [2024-04-17 07:10:42.172][biodb::testThat]
biodb.INFO [2024-04-17 07:10:42.173][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-17 07:10:42.174][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:42.175][biodb::testThat]
biodb.INFO [2024-04-17 07:10:42.184][biodb::testThat]
biodb.INFO [2024-04-17 07:10:42.185][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-17 07:10:42.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:42.187][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:42.191][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-04-17 07:10:43.105][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-04-17 07:10:43.701][biodb::testThat]
biodb.INFO [2024-04-17 07:10:43.702][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-17 07:10:43.703][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:43.704][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:43.816][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[2024-04-17 07:10:43.940][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:43.941][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:43.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:43.943][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:43.944][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:43.945][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:43.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:43.946][ef$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:43.949][biodb::testThat]
biodb.INFO [2024-04-17 07:10:43.951][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-04-17 07:10:43.952][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:43.953][biodb::testThat]
biodb.TRACE[2024-04-17 07:10:43.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:43.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:43.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:43.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:43.969][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:43.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:43.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:43.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:43.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:43.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:43.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:43.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:44.069][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[2024-04-17 07:10:44.073][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:44.074][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-17 07:10:44.076][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:44.077][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-17 07:10:44.160][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[2024-04-17 07:10:44.164][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:44.165][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-17 07:10:44.166][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:44.168][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-04-17 07:10:44.183][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-17 07:10:44.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-17 07:10:44.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:44.223][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[2024-04-17 07:10:44.227][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:44.228][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-04-17 07:10:44.229][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:44.232][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-04-17 07:10:44.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:44.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:44.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:44.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:44.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:44.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:44.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:44.246][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-04-17 07:10:44.300][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:44.302][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-04-17 07:10:44.303][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:44.304][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:44.305][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:44.306][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:44.307][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:44.308][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:44.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:44.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:44.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:44.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:44.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:44.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:44.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:44.322][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-04-17 07:10:44.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:44.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:44.327][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-04-17 07:10:44.446][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-04-17 07:10:44.545][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:44.548][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-04-17 07:10:44.562][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-04-17 07:10:44.566][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-04-17 07:10:44.567][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:44.569][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:44.570][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:44.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:44.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:44.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:44.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:44.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:44.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:44.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:44.586][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:44.587][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:44.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.589][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:44.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:44.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.594][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:44.595][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:44.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.596][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.597][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:44.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:44.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.601][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:44.602][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:44.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.603][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.605][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:44.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:44.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.609][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:44.610][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:44.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.611][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:44.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:44.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.615][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:44.618][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:44.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.620][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:44.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:44.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.625][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:44.626][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:44.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.628][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.629][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:44.630][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.632][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.633][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:44.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.636][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:44.637][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:44.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.639][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:44.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:44.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.644][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:44.645][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:44.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.646][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:44.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:44.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.652][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:44.653][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:44.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.656][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.658][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:44.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:44.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.662][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:44.663][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:44.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.665][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.666][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:44.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:44.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:44.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:44.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:44.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:44.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:44.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:44.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:44.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:44.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:44.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:44.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:44.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:44.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:44.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:44.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:44.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:44.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:44.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:44.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:44.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:44.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:44.717][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-04-17 07:10:44.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:44.740][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[2024-04-17 07:10:44.743][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:44.745][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-04-17 07:10:44.746][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:44.749][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-04-17 07:10:44.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:44.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:44.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:44.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:44.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:44.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:44.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:44.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:44.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:44.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:44.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:44.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:44.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:44.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:44.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:44.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:44.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:44.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:44.800][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-04-17 07:10:44.801][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:44.802][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-04-17 07:10:44.803][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:44.804][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:44.805][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:44.806][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:44.807][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:44.808][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:44.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:44.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:44.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:44.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:44.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:44.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:44.833][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[2024-04-17 07:10:44.834][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-04-17 07:10:44.858][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:44.859][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:44.874][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-04-17 07:10:44.959][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-04-17 07:10:45.040][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:45.042][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-04-17 07:10:45.046][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-04-17 07:10:45.049][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-04-17 07:10:45.051][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:45.052][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:45.053][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:45.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:45.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:45.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:45.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:45.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:45.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:45.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:45.068][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.069][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.070][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.075][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:45.076][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:45.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.078][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.079][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:45.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:45.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.082][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:45.084][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:45.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.087][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:45.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:45.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.093][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:45.093][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:45.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.095][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:45.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:45.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.100][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:45.101][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:45.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.104][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:45.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:45.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.109][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:45.110][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:45.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.112][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.113][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:45.114][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.115][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.116][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:45.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.121][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:45.123][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:45.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.124][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:45.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:45.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.129][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:45.130][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:45.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.132][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:45.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:45.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.136][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:45.137][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:45.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.139][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.140][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:45.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:45.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.143][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:45.144][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:45.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.146][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.147][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:45.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:45.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:45.202][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-04-17 07:10:45.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:45.233][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[2024-04-17 07:10:45.236][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:45.238][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-17 07:10:45.239][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:45.240][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-17 07:10:45.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:45.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:45.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:45.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:45.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:45.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:45.254][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:45.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:45.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:45.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:45.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:45.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:45.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:45.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:45.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:45.278][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-04-17 07:10:45.279][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:45.281][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-04-17 07:10:45.282][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:45.283][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:45.285][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:45.287][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:45.288][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:45.289][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:45.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:45.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:45.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:45.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:45.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:45.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:45.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:45.303][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-04-17 07:10:45.306][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:45.307][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:45.308][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-04-17 07:10:45.421][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-04-17 07:10:45.496][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:45.500][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-04-17 07:10:45.504][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-04-17 07:10:45.507][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-04-17 07:10:45.509][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:45.510][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:45.511][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:45.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:45.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:45.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:45.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:45.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:45.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:45.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:45.526][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.527][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.529][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.533][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:45.534][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:45.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.536][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.537][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:45.538][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:45.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.539][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.540][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:45.548][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:45.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.553][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.555][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:45.556][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:45.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.557][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.559][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:45.560][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:45.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.561][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.562][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:45.563][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.565][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.566][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:45.567][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:45.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.568][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.569][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:45.570][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:45.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.572][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:45.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:45.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.579][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:45.580][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:45.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.582][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.583][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:45.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:45.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.587][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:45.588][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:45.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.589][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:45.630][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-04-17 07:10:45.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:45.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:45.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:45.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:45.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:45.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:45.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:45.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:45.661][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-04-17 07:10:45.662][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:45.664][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-04-17 07:10:45.665][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:45.667][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:45.668][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:45.670][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:45.670][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:45.671][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:45.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:45.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:45.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:45.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:45.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:45.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:45.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:45.685][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-04-17 07:10:45.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:45.689][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:45.691][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-04-17 07:10:45.807][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-04-17 07:10:45.882][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:45.885][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-04-17 07:10:45.889][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-04-17 07:10:45.892][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-04-17 07:10:45.894][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:45.895][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:45.896][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:45.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:45.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:45.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:45.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:45.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:45.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:45.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:45.920][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.922][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.923][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.928][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:45.929][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:45.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.931][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.933][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:45.934][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:45.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.936][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.939][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:45.941][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:45.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.943][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.944][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:45.945][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:45.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.947][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.948][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:45.949][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:45.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.951][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.952][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:45.953][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:45.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.954][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.955][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:45.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:45.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.958][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.959][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:45.960][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:45.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.961][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:45.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:45.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.966][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:45.967][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:45.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.969][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.970][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:45.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:45.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.973][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:45.974][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:45.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.976][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:45.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:45.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:45.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:45.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:45.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:46.019][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-04-17 07:10:46.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:46.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:46.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:46.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:46.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:46.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:46.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:46.052][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[2024-04-17 07:10:46.054][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-04-17 07:10:46.054][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:46.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-04-17 07:10:46.057][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:46.058][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:46.059][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:46.060][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:46.061][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:46.062][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:46.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:46.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:46.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:46.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:46.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:46.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:46.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:46.076][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-04-17 07:10:46.079][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:46.080][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:46.081][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-04-17 07:10:46.190][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-04-17 07:10:46.266][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:46.269][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-04-17 07:10:46.273][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-04-17 07:10:46.276][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-04-17 07:10:46.278][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:46.279][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:46.280][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:46.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:46.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:46.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:46.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:46.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:46.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:46.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:46.295][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.296][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.297][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.302][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:46.303][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:46.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.305][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.307][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:46.308][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:46.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.310][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.312][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:46.313][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:46.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.314][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.315][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:46.316][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:46.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.318][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.319][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:46.320][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:46.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.321][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.323][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:46.324][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.325][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.326][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:46.327][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:46.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.329][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.330][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:46.331][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:46.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.332][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.334][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:46.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:46.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.338][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:46.338][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:46.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.340][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.341][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:46.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:46.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.345][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:46.346][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:46.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.347][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:46.384][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-04-17 07:10:46.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:46.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:46.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:46.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:46.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:46.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:46.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:46.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:46.414][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-04-17 07:10:46.415][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:46.417][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-04-17 07:10:46.418][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:46.419][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:46.426][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:46.429][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:46.430][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:46.431][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:46.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:46.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:46.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:46.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:46.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:46.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:46.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:46.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-04-17 07:10:46.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:46.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:46.451][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-04-17 07:10:46.525][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-04-17 07:10:46.606][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:46.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-04-17 07:10:46.615][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-04-17 07:10:46.618][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-04-17 07:10:46.619][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:46.620][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:46.621][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:46.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:46.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:46.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:46.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:46.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:46.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:46.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:46.635][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.636][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.638][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.642][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:46.643][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:46.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.645][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.646][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:46.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:46.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.649][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:46.650][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:46.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.652][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.654][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:46.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:46.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.659][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:46.660][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:46.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.662][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:46.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:46.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.667][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:46.668][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:46.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.669][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:46.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:46.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.674][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:46.675][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:46.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.677][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.678][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:46.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:46.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.682][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:46.683][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.684][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.686][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:46.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.689][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:46.690][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:46.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.691][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:46.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:46.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.697][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:46.698][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:46.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.702][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:46.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:46.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.709][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:46.710][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:46.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.712][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.713][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:46.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:46.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.716][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:46.717][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:46.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.719][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.720][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:46.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:46.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:46.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:46.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:46.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:46.768][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-04-17 07:10:46.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:46.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:46.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:46.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:46.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:46.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:46.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:46.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:46.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:46.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:46.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:46.793][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-04-17 07:10:46.794][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:46.795][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-04-17 07:10:46.797][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:46.798][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:46.799][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:46.800][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:46.801][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:46.801][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:46.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:46.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:46.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:46.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:46.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:46.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:46.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:46.816][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-04-17 07:10:46.822][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:46.824][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:46.826][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-04-17 07:10:46.898][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-04-17 07:10:46.980][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:46.983][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-04-17 07:10:46.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-04-17 07:10:46.990][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-04-17 07:10:46.992][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:46.993][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:46.994][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:46.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:46.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:46.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:47.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:47.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:47.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:47.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:47.007][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.008][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.010][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.015][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:47.016][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:47.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.018][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.021][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:47.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:47.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.026][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:47.027][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:47.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.028][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.030][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:47.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:47.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.033][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:47.034][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:47.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.036][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.037][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:47.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:47.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.040][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.041][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.043][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.047][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:47.048][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:47.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.049][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.050][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:47.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:47.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.054][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:47.055][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.056][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.057][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:47.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.061][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.061][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.063][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.067][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:47.080][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:47.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.082][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:47.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:47.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.088][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:47.089][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:47.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.090][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.092][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:47.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:47.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.095][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:47.096][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:47.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.097][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.100][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:47.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:47.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:47.141][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-04-17 07:10:47.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:47.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:47.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:47.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:47.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:47.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:47.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:47.164][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[2024-04-17 07:10:47.165][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-04-17 07:10:47.165][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:47.167][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-04-17 07:10:47.168][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:47.169][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:47.171][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:47.173][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:47.174][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:47.176][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:47.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:47.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:47.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:47.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:47.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:47.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:47.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:47.190][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-04-17 07:10:47.193][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:47.194][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:47.195][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-04-17 07:10:47.270][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-04-17 07:10:47.346][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:47.349][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-04-17 07:10:47.353][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-04-17 07:10:47.356][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-04-17 07:10:47.357][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:47.358][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:47.360][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:47.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:47.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:47.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:47.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:47.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:47.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:47.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:47.373][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.374][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.375][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.380][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:47.381][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:47.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.382][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.383][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:47.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:47.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.388][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:47.389][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:47.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.398][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.403][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:47.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:47.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.407][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:47.408][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:47.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.409][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:47.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:47.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.414][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.414][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.416][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.420][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:47.421][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:47.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.424][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.426][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:47.428][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.429][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.431][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:47.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.434][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.435][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.437][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.441][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:47.442][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:47.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.443][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:47.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:47.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.448][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:47.449][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:47.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.450][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.452][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:47.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:47.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.455][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:47.456][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:47.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.457][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.459][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:47.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:47.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:47.506][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-04-17 07:10:47.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:47.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:47.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:47.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:47.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:47.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:47.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:47.528][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[2024-04-17 07:10:47.529][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-04-17 07:10:47.530][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:47.532][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-04-17 07:10:47.533][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:47.534][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:47.535][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:47.536][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:47.537][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:47.538][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:47.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:47.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:47.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:47.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:47.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:47.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:47.550][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[2024-04-17 07:10:47.552][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-04-17 07:10:47.555][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:47.556][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:47.557][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-04-17 07:10:47.636][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-04-17 07:10:47.722][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:47.725][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-04-17 07:10:47.729][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-04-17 07:10:47.731][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-04-17 07:10:47.734][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:47.735][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:47.736][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:47.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:47.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:47.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:47.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:47.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:47.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:47.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:47.750][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.752][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.753][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.759][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:47.761][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:47.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.763][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.765][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:47.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:47.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.768][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:47.769][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:47.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.771][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:47.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:47.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.777][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:47.778][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:47.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.780][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:47.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:47.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.786][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.787][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.788][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:47.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.793][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:47.794][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:47.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.796][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.797][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:47.798][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.799][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.800][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:47.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.804][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.805][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.806][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:47.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.811][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:47.812][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:47.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.814][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:47.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:47.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.821][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:47.822][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:47.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.823][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.825][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:47.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:47.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.828][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:47.829][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:47.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.830][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.832][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:47.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:47.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:47.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:47.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:47.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:47.871][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-04-17 07:10:47.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:47.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:47.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:47.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:47.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:47.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:47.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:47.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:47.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:47.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:47.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:47.904][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-04-17 07:10:47.905][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:47.906][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-04-17 07:10:47.908][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:47.909][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:47.910][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:47.911][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:47.911][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:47.912][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:47.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:47.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:47.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:47.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:47.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:47.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:47.927][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[2024-04-17 07:10:47.928][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-04-17 07:10:47.932][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:47.933][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:47.934][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-04-17 07:10:48.008][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-04-17 07:10:48.086][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:48.089][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-04-17 07:10:48.093][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-04-17 07:10:48.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-04-17 07:10:48.097][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:48.099][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:48.100][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:48.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:48.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:48.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:48.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:48.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:48.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:48.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:48.113][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.114][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.116][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.121][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:48.121][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:48.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.123][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.124][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:48.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:48.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.129][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:48.131][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:48.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.133][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:48.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:48.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.137][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:48.138][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:48.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.140][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:48.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:48.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.144][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.145][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.147][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.151][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:48.152][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:48.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.153][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.155][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:48.155][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.157][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.158][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:48.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.161][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.162][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.164][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.171][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:48.172][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:48.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.174][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:48.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:48.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.179][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:48.180][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:48.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.181][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:48.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:48.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.186][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:48.187][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:48.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.188][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.189][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:48.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:48.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:48.239][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-04-17 07:10:48.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:48.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:48.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:48.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:48.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:48.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:48.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:48.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:48.264][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-04-17 07:10:48.264][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:48.266][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-04-17 07:10:48.267][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:48.268][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:48.269][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:48.270][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:48.271][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:48.272][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:48.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:48.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:48.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:48.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:48.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:48.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:48.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:48.288][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-04-17 07:10:48.293][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:48.294][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:48.296][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-04-17 07:10:48.390][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-04-17 07:10:48.465][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:48.468][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-04-17 07:10:48.472][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-04-17 07:10:48.475][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-04-17 07:10:48.476][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:48.477][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:48.479][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:48.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:48.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:48.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:48.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:48.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:48.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:48.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:48.497][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.498][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.501][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.507][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:48.507][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:48.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.509][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.510][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:48.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:48.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.514][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:48.515][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:48.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.517][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.519][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:48.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:48.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.524][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:48.525][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:48.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.527][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:48.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:48.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.532][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.533][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.534][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.538][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:48.540][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:48.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.542][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.543][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:48.544][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.546][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.547][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:48.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.593][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.594][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.596][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.603][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:48.604][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:48.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.606][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:48.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:48.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.611][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:48.612][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:48.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.613][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.614][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:48.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:48.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.618][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:48.618][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:48.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.620][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.621][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:48.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:48.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:48.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:48.657][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-04-17 07:10:48.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:48.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:48.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:48.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:48.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:48.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:48.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:48.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:48.682][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-04-17 07:10:48.683][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:48.685][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-04-17 07:10:48.686][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:48.687][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:48.688][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:48.689][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:48.690][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:48.691][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:48.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:48.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:48.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:48.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:48.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:48.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:48.706][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[2024-04-17 07:10:48.707][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-04-17 07:10:48.710][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:48.711][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:48.713][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-04-17 07:10:48.813][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-04-17 07:10:48.891][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:48.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-04-17 07:10:48.899][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-04-17 07:10:48.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-04-17 07:10:48.903][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:48.904][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:48.905][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:48.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:48.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:48.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:48.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:48.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:48.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:48.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:48.924][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.925][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.927][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:48.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:48.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.932][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:48.940][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:48.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.947][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.948][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:48.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:48.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.952][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:48.953][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:48.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.954][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.955][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:48.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:48.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.960][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:48.961][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:48.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.963][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:48.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:48.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.967][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.968][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.970][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.971][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:48.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.974][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:48.975][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:48.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.977][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.978][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:48.979][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.980][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.981][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:48.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:48.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.985][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.986][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.987][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:48.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.991][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:48.994][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:48.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.995][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:48.997][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:48.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:48.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:48.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.000][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:49.001][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:49.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.002][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.004][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:49.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:49.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.007][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:49.008][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:49.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.009][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.010][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:49.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:49.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:49.051][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-04-17 07:10:49.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:49.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:49.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:49.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:49.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:49.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:49.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:49.074][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[2024-04-17 07:10:49.075][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-04-17 07:10:49.076][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:49.077][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-04-17 07:10:49.078][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:49.079][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:49.080][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:49.081][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:49.082][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:49.083][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:49.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:49.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:49.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:49.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:49.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:49.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:49.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:49.104][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-04-17 07:10:49.108][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:49.109][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:49.110][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-04-17 07:10:49.183][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-04-17 07:10:49.259][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:49.261][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-04-17 07:10:49.265][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-04-17 07:10:49.268][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-04-17 07:10:49.270][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:49.271][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:49.272][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:49.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:49.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:49.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:49.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:49.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:49.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:49.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:49.286][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.287][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.289][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.293][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:49.294][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:49.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.296][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.298][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:49.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:49.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.301][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:49.302][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:49.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.304][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:49.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:49.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.311][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:49.312][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:49.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.314][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.315][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:49.316][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:49.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.317][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.318][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:49.319][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:49.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.321][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.322][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:49.323][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.324][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.325][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:49.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.329][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:49.330][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:49.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.331][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:49.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:49.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.336][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:49.336][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:49.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.338][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:49.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:49.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.342][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:49.343][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:49.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.345][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.346][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:49.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:49.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.349][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:49.351][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:49.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.353][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:49.391][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-04-17 07:10:49.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:49.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:49.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:49.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:49.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:49.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:49.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:49.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:49.425][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-04-17 07:10:49.426][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:49.427][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-04-17 07:10:49.429][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:49.430][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:49.431][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:49.432][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:49.434][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:49.435][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:49.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:49.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:49.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:49.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:49.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:49.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:49.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:49.448][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-04-17 07:10:49.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:49.453][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:49.455][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-04-17 07:10:49.538][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-04-17 07:10:49.616][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:49.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-04-17 07:10:49.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-04-17 07:10:49.627][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-04-17 07:10:49.629][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:49.630][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:49.631][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:49.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:49.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:49.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:49.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:49.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:49.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:49.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:49.646][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.647][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.648][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.653][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:49.654][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:49.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.656][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.657][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:49.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:49.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.661][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:49.662][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:49.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.664][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.665][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:49.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:49.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.668][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:49.669][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:49.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.671][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.672][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:49.673][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:49.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.676][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.678][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:49.679][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:49.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.681][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.682][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:49.683][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.685][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.686][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:49.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.690][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:49.690][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:49.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.692][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:49.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:49.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.697][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:49.698][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:49.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.699][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:49.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:49.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.704][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:49.705][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:49.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.708][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.709][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:49.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:49.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.713][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:49.714][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:49.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.716][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:49.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:49.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:49.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:49.776][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-04-17 07:10:49.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:49.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:49.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:49.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:49.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:49.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:49.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:49.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:49.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:49.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:49.797][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[2024-04-17 07:10:49.798][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-04-17 07:10:49.799][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:49.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-04-17 07:10:49.802][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:49.803][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:49.804][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:49.805][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:49.806][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:49.807][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:49.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:49.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:49.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:49.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:49.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:49.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:49.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:49.821][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-04-17 07:10:49.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:49.825][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:49.826][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-04-17 07:10:49.927][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-04-17 07:10:50.011][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:50.014][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-04-17 07:10:50.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-04-17 07:10:50.022][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-04-17 07:10:50.024][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:50.025][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:50.026][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:50.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:50.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:50.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:50.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:50.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:50.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:50.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:50.042][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.044][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.045][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.052][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:50.054][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:50.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.055][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.057][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:50.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:50.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.060][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:50.061][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:50.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.063][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.064][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:50.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:50.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.067][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:50.068][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:50.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.070][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:50.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:50.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.074][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.075][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.076][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.081][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:50.082][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:50.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.083][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.085][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:50.086][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.087][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.088][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:50.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.094][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.096][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.097][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.102][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:50.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:50.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.104][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:50.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:50.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.109][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:50.110][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:50.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.123][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.125][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:50.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:50.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.128][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:50.131][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:50.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.133][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:50.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:50.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:50.176][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-04-17 07:10:50.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:50.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:50.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:50.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:50.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:50.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:50.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:50.199][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[2024-04-17 07:10:50.200][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-04-17 07:10:50.201][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:50.202][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-04-17 07:10:50.203][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:50.204][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:50.205][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:50.206][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:50.207][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:50.208][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:50.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:50.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:50.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:50.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:50.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:50.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:50.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:50.223][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-04-17 07:10:50.227][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:50.228][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:50.229][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-04-17 07:10:50.300][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-04-17 07:10:50.372][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:50.376][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-04-17 07:10:50.380][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-04-17 07:10:50.383][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-04-17 07:10:50.384][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:50.386][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:50.387][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:50.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:50.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:50.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:50.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:50.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:50.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:50.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:50.401][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.402][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.403][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.408][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:50.410][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:50.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.412][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.413][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:50.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:50.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.417][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:50.418][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:50.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.420][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.421][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:50.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:50.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.424][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:50.425][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:50.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.426][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:50.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:50.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.445][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.446][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.448][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.453][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:50.454][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:50.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.455][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.456][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:50.457][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.459][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.460][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:50.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.464][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.465][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.466][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.471][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:50.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:50.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.473][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:50.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:50.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.480][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:50.481][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:50.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.483][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.484][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:50.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:50.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.487][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:50.488][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:50.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.490][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.491][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:50.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:50.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:50.531][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-04-17 07:10:50.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:50.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:50.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:50.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:50.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:50.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:50.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:50.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:50.555][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-04-17 07:10:50.556][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:50.557][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-04-17 07:10:50.559][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:50.560][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:50.561][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:50.562][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:50.562][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:50.563][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:50.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:50.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:50.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:50.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:50.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:50.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:50.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:50.577][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-04-17 07:10:50.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:50.581][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:50.583][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-04-17 07:10:50.688][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-04-17 07:10:50.767][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:50.770][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-04-17 07:10:50.774][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-04-17 07:10:50.777][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-04-17 07:10:50.778][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:50.780][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:50.781][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:50.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:50.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:50.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:50.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:50.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:50.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:50.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:50.805][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.806][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.808][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.812][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:50.813][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:50.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.815][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.816][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:50.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.822][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:50.824][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:50.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.826][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.828][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:50.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:50.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.831][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:50.832][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:50.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.834][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:50.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:50.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.838][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.839][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.840][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.842][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:50.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.845][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:50.846][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:50.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.847][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.848][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:50.849][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.851][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.852][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:50.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.855][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.856][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.857][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:50.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.862][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:50.863][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:50.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.864][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:50.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:50.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.870][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:50.871][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:50.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.872][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.873][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:50.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:50.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.877][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:50.878][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:50.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.879][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.880][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:50.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:50.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:50.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:50.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:50.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:50.920][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-04-17 07:10:50.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:50.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:50.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:50.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:50.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:50.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:50.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:50.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:50.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:50.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:50.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:50.950][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-04-17 07:10:50.952][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:50.954][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-04-17 07:10:50.955][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:50.956][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:50.957][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:50.958][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:50.959][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:50.959][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:50.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:50.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:50.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:50.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:50.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:50.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:50.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:50.975][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-04-17 07:10:50.979][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:50.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:50.981][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-04-17 07:10:51.272][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-04-17 07:10:51.346][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:51.349][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-04-17 07:10:51.353][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-04-17 07:10:51.355][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-04-17 07:10:51.357][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:51.358][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:51.359][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:51.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:51.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:51.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:51.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:51.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:51.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:51.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:51.373][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.374][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.376][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.380][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:51.381][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:51.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.383][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.384][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:51.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:51.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.387][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:51.388][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:51.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.390][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:51.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:51.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.398][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:51.399][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:51.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.401][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:51.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:51.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.406][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:51.407][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:51.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.408][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:51.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:51.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.413][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:51.414][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:51.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.415][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.417][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:51.418][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.419][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.421][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:51.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.424][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:51.425][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:51.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.428][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:51.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:51.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.434][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:51.435][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:51.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.436][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:51.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:51.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.441][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:51.442][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:51.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.443][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.444][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:51.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:51.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.448][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:51.448][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:51.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.450][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.451][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:51.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:51.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:51.507][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-04-17 07:10:51.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:51.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:51.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:51.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:51.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:51.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:51.529][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:51.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:51.530][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-04-17 07:10:51.531][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:51.533][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-04-17 07:10:51.534][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:51.535][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:51.537][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:51.538][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:51.539][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:51.539][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:51.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:51.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:51.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:51.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:51.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:51.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:51.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:51.553][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-04-17 07:10:51.556][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:51.556][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:51.559][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-04-17 07:10:51.673][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-04-17 07:10:51.747][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:51.750][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-04-17 07:10:51.754][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-04-17 07:10:51.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-04-17 07:10:51.759][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:51.760][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:51.761][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:51.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:51.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:51.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:51.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:51.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:51.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:51.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:51.775][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.776][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.778][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.782][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:51.784][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:51.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.786][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:51.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:51.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.791][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:51.792][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:51.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.794][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.795][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:51.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:51.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.798][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:51.799][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:51.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.801][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:51.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:51.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.805][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:51.806][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:51.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.807][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:51.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:51.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.812][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:51.813][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:51.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.815][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.817][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:51.819][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.820][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.822][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:51.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.825][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:51.827][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:51.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.828][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:51.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:51.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.833][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:51.834][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:51.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.846][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:51.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:51.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.852][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:51.853][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:51.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.854][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.856][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:51.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:51.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.860][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:51.861][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:51.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.863][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.864][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:51.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:51.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:51.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:51.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:51.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:51.905][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-04-17 07:10:51.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:51.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:51.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:51.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:51.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:51.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:51.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:51.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:51.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:51.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:51.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:51.927][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-04-17 07:10:51.927][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:51.929][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-04-17 07:10:51.930][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:10:51.931][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:10:51.933][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:51.935][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:51.936][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:10:51.937][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:10:51.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:51.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:51.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:51.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:51.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:51.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:51.951][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[2024-04-17 07:10:51.952][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-04-17 07:10:51.955][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:10:51.956][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:10:51.958][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-04-17 07:10:52.047][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-04-17 07:10:52.120][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:10:52.123][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-04-17 07:10:52.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-04-17 07:10:52.130][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-04-17 07:10:52.134][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:10:52.135][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:52.137][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:52.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:52.153][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.154][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.156][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.160][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:52.161][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:52.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.162][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.163][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:52.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:52.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.167][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:52.167][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:52.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.169][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.170][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:52.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:52.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.185][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:52.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:52.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.189][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.191][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:52.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:52.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.195][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:52.196][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:52.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.198][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:52.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:52.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.203][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:52.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:52.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.205][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.206][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:52.207][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.209][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.210][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:52.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.215][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.216][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.218][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.223][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:52.224][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:52.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.225][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:52.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:52.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.231][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:52.231][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:52.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.233][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.234][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:52.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:52.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.237][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:52.238][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:52.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.240][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.241][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:52.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:52.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.277][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-04-17 07:10:52.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:52.299][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-04-17 07:10:52.300][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:52.301][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-04-17 07:10:52.302][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:52.305][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2024-04-17 07:10:52.306][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:52.307][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:52.308][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:52.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:52.322][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.323][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.324][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.329][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:52.329][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:52.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.338][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.340][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:52.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:52.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.344][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:52.345][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:52.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.346][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.347][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:52.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:52.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.351][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:52.352][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:52.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.353][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:52.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:52.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.357][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:52.358][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:52.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.360][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:52.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:52.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.364][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:52.365][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:52.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.367][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.368][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:52.369][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.370][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.371][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:52.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.374][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.375][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.377][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.381][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:52.382][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:52.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.383][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:52.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:52.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.388][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:52.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:52.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.390][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.391][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:52.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:52.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.394][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:52.395][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:52.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.397][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.398][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:52.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:52.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:52.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:52.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:52.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.432][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-04-17 07:10:52.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.462][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[2024-04-17 07:10:52.465][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:52.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-17 07:10:52.468][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:52.469][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-17 07:10:52.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:52.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.510][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[2024-04-17 07:10:52.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.536][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[2024-04-17 07:10:52.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.563][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:52.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:52.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.611][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:52.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:52.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.659][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:52.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.678][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[2024-04-17 07:10:52.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.699][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.TRACE[2024-04-17 07:10:52.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:52.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.740][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:52.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:52.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.780][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:52.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:52.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.831][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[2024-04-17 07:10:52.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.853][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[2024-04-17 07:10:52.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.875][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.TRACE[2024-04-17 07:10:52.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.895][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[2024-04-17 07:10:52.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:52.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:52.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:52.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:52.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:52.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:52.915][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.TRACE[2024-04-17 07:10:52.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:52.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:52.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:52.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:52.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:52.993][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[2024-04-17 07:10:52.997][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:52.998][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2024-04-17 07:10:52.999][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:53.002][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2024-04-17 07:10:53.005][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[2024-04-17 07:10:53.008][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:53.010][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2024-04-17 07:10:53.011][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:53.012][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2024-04-17 07:10:53.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:53.025][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-04-17 07:10:53.026][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:53.028][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-04-17 07:10:53.029][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:53.030][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2024-04-17 07:10:53.031][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:53.033][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:53.034][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:53.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:53.048][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.049][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.050][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.055][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:53.056][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:53.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.057][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.058][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:53.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:53.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.062][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:53.063][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:53.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.064][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.065][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:53.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:53.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.069][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:53.070][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:53.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.071][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:53.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:53.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.075][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:53.076][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:53.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.078][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:53.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:53.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.082][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:53.083][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:53.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.084][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.085][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:53.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:53.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.088][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:53.089][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:53.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.091][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.092][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:53.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:53.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.095][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.096][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.098][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.110][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:53.111][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:53.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.113][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.114][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:53.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:53.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.118][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:53.118][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:53.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.120][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.121][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:53.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:53.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.124][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:53.125][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:53.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.127][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:53.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:53.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.163][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-04-17 07:10:53.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.184][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:53.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.204][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[2024-04-17 07:10:53.205][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-04-17 07:10:53.206][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:53.207][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-04-17 07:10:53.209][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:53.211][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2024-04-17 07:10:53.213][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:53.214][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:53.215][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:53.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:53.229][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.231][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.232][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.237][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:53.238][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:53.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.239][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.240][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:53.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:53.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.244][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:53.245][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:53.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.247][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.248][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:53.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:53.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.251][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:53.252][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:53.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.262][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:53.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:53.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.267][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:53.268][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:53.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.269][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:53.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:53.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.274][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:53.275][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:53.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.277][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.278][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:53.279][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:53.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.280][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.281][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:53.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:53.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.285][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.286][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.287][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.292][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:53.293][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:53.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.294][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:53.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:53.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.299][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:53.300][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:53.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.301][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.302][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:53.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:53.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.306][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:53.306][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:53.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.308][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.309][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:53.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:53.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:53.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:53.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:53.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.345][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-04-17 07:10:53.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.376][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[2024-04-17 07:10:53.380][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:53.381][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-17 07:10:53.383][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:53.384][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-17 07:10:53.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.397][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:53.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:53.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.454][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:53.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.482][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.TRACE[2024-04-17 07:10:53.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.509][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.TRACE[2024-04-17 07:10:53.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.532][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.TRACE[2024-04-17 07:10:53.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.553][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.TRACE[2024-04-17 07:10:53.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:53.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.604][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.TRACE[2024-04-17 07:10:53.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:53.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.645][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.TRACE[2024-04-17 07:10:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.666][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.TRACE[2024-04-17 07:10:53.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.687][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:53.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.708][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.TRACE[2024-04-17 07:10:53.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.745][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.TRACE[2024-04-17 07:10:53.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:53.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.790][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:53.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.811][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.TRACE[2024-04-17 07:10:53.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.832][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:53.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.853][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[2024-04-17 07:10:53.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.884][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[2024-04-17 07:10:53.888][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:53.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-17 07:10:53.890][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:53.892][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-17 07:10:53.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:53.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.937][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.TRACE[2024-04-17 07:10:53.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.965][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.TRACE[2024-04-17 07:10:53.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:53.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:53.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:53.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:53.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:53.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:53.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:53.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:53.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:53.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:53.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:53.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.040][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[2024-04-17 07:10:54.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.095][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.TRACE[2024-04-17 07:10:54.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.158][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[2024-04-17 07:10:54.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.178][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:54.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.255][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.TRACE[2024-04-17 07:10:54.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.387][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-17 07:10:54.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-17 07:10:54.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:54.407][biodb::testThat]
biodb.INFO [2024-04-17 07:10:54.408][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-04-17 07:10:54.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:54.410][biodb::testThat]
biodb.TRACE[2024-04-17 07:10:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-17 07:10:54.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-17 07:10:54.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.445][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[2024-04-17 07:10:54.447][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[2024-04-17 07:10:54.451][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:54.452][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-04-17 07:10:54.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:54.455][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-04-17 07:10:54.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.479][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[2024-04-17 07:10:54.483][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:54.484][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-04-17 07:10:54.485][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:54.486][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-04-17 07:10:54.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.500][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.TRACE[2024-04-17 07:10:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.520][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:54.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:54.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.531][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:10:54.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.549][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.550][private$selectFields]
biodb.TRACE[2024-04-17 07:10:54.551][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:54.552][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:54.552][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.553][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.554][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.555][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.556][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.557][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.559][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.559][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.560][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.561][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.569][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.572][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.573][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:54.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.593][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-04-17 07:10:54.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.612][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.613][private$selectFields]
biodb.TRACE[2024-04-17 07:10:54.613][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:54.614][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:54.615][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.616][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.617][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.618][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.619][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.620][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.621][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.622][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.623][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.624][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.625][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.626][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.627][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:54.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.638][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-17 07:10:54.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.657][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.657][private$selectFields]
biodb.TRACE[2024-04-17 07:10:54.658][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:54.659][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:54.660][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.661][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.662][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.663][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.664][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.665][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.666][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.668][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.669][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.669][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.670][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.672][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.673][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:54.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.684][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-04-17 07:10:54.685][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:10:54.686][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-17 07:10:54.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:54.790][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[2024-04-17 07:10:54.794][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:54.795][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-04-17 07:10:54.796][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:54.798][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-04-17 07:10:54.802][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[2024-04-17 07:10:54.805][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:54.807][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-04-17 07:10:54.808][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:54.810][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-04-17 07:10:54.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.822][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[2024-04-17 07:10:54.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.845][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.TRACE[2024-04-17 07:10:54.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.868][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.TRACE[2024-04-17 07:10:54.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:54.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:54.915][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:10:54.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:54.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.959][private$selectFields]
biodb.TRACE[2024-04-17 07:10:54.960][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:54.961][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:54.962][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.963][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.964][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.965][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.966][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.967][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.969][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.969][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.970][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:54.971][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.972][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.973][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.974][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:54.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:54.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:54.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:54.987][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-04-17 07:10:54.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:54.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:54.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:54.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:54.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:54.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:54.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:55.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.051][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.052][private$selectFields]
biodb.TRACE[2024-04-17 07:10:55.053][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:55.054][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:55.055][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.056][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.057][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.059][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.059][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.060][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.062][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.063][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.073][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.074][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.075][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.077][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.079][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:55.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.093][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-17 07:10:55.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.104][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:55.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.113][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.115][private$selectFields]
biodb.TRACE[2024-04-17 07:10:55.116][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:55.117][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:55.118][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.119][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.120][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.122][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.123][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.123][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.125][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.126][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.127][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.128][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.128][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.130][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.131][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:55.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.142][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-04-17 07:10:55.143][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:10:55.144][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-17 07:10:55.156][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-17 07:10:55.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-17 07:10:55.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:55.164][biodb::testThat]
biodb.INFO [2024-04-17 07:10:55.166][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-04-17 07:10:55.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:55.167][biodb::testThat]
biodb.TRACE[2024-04-17 07:10:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-17 07:10:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-17 07:10:55.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.215][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.DEBUG[2024-04-17 07:10:55.218][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[2024-04-17 07:10:55.223][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:55.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-04-17 07:10:55.226][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:55.227][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-04-17 07:10:55.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.243][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:55.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.258][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[2024-04-17 07:10:55.261][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:55.263][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-04-17 07:10:55.264][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:55.265][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-04-17 07:10:55.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:55.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.300][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.TRACE[2024-04-17 07:10:55.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.316][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:10:55.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:55.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.337][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.337][private$selectFields]
biodb.TRACE[2024-04-17 07:10:55.338][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:55.339][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:55.340][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.340][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.343][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.344][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.345][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.346][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.347][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.348][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.349][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.349][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.351][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.352][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:55.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.365][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-04-17 07:10:55.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:55.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.397][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.397][private$selectFields]
biodb.TRACE[2024-04-17 07:10:55.398][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:55.399][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:55.400][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.403][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.404][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.405][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.406][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.407][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.408][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.411][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.412][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:55.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.425][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-17 07:10:55.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:55.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.445][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.446][private$selectFields]
biodb.TRACE[2024-04-17 07:10:55.446][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:55.447][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:55.448][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.449][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.450][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.451][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.452][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.454][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.456][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.457][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.458][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.459][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.460][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.462][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.463][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:55.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.475][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-04-17 07:10:55.476][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:10:55.477][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-17 07:10:55.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:55.518][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[2024-04-17 07:10:55.522][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:55.523][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-04-17 07:10:55.525][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:55.526][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-04-17 07:10:55.530][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[2024-04-17 07:10:55.533][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:55.534][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-04-17 07:10:55.536][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:55.539][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-04-17 07:10:55.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:55.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.587][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.TRACE[2024-04-17 07:10:55.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.609][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:55.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:55.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.620][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:10:55.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.631][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:55.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.642][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.643][private$selectFields]
biodb.TRACE[2024-04-17 07:10:55.644][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:55.644][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:55.645][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.646][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.647][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.648][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.649][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.650][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.652][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.652][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.653][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.654][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.656][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.658][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.660][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:55.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.672][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-04-17 07:10:55.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:55.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.691][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.692][private$selectFields]
biodb.TRACE[2024-04-17 07:10:55.693][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:55.694][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:55.695][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.696][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.696][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.698][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.699][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.700][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.701][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.702][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.703][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.704][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.705][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.706][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.707][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:55.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.727][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-17 07:10:55.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:55.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.749][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.750][private$selectFields]
biodb.TRACE[2024-04-17 07:10:55.751][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:55.752][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:55.752][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.753][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.754][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.756][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.757][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.759][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.762][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.764][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.765][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.766][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.767][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.768][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.769][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:55.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.780][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-04-17 07:10:55.781][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:10:55.782][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-17 07:10:55.791][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-17 07:10:55.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-17 07:10:55.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:55.799][biodb::testThat]
biodb.INFO [2024-04-17 07:10:55.800][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-04-17 07:10:55.801][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:55.801][biodb::testThat]
biodb.TRACE[2024-04-17 07:10:55.804][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-17 07:10:55.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-17 07:10:55.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:55.847][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[2024-04-17 07:10:55.851][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:55.853][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-04-17 07:10:55.855][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:55.857][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-04-17 07:10:55.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:55.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.890][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[2024-04-17 07:10:55.894][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:55.895][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-04-17 07:10:55.896][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:55.897][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-04-17 07:10:55.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.923][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:55.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.945][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:55.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:55.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:55.959][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:10:55.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:55.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:55.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:55.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:55.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:55.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:55.971][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:55.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.980][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.981][private$selectFields]
biodb.TRACE[2024-04-17 07:10:55.982][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:55.983][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:55.984][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.985][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.985][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.987][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.988][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.989][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.990][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.991][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.993][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:55.994][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.995][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:55.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:55.998][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:55.999][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:56.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.010][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-04-17 07:10:56.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:56.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.031][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.033][private$selectFields]
biodb.TRACE[2024-04-17 07:10:56.033][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:56.035][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:56.036][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.037][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.038][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.039][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.040][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.041][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.043][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.043][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.044][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.045][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.046][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.047][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.048][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:56.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.060][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-17 07:10:56.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.080][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:56.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.091][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.092][private$selectFields]
biodb.TRACE[2024-04-17 07:10:56.093][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:56.094][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:56.095][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.096][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.097][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.099][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.100][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.101][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.103][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.104][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.105][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.109][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.110][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.122][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-04-17 07:10:56.123][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:10:56.123][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-17 07:10:56.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:56.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.177][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[2024-04-17 07:10:56.180][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[2024-04-17 07:10:56.183][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:56.184][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-04-17 07:10:56.185][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:56.187][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-04-17 07:10:56.190][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[2024-04-17 07:10:56.193][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:56.195][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-04-17 07:10:56.197][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:56.199][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-04-17 07:10:56.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.212][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[2024-04-17 07:10:56.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:56.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.232][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:10:56.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:56.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.267][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[2024-04-17 07:10:56.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:56.278][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:10:56.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:56.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.300][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.300][private$selectFields]
biodb.TRACE[2024-04-17 07:10:56.301][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:56.302][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:56.303][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.304][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.305][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.306][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.307][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.312][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.315][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.316][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.317][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.318][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.319][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.320][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.321][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:56.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.332][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-04-17 07:10:56.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:56.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.351][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.352][private$selectFields]
biodb.TRACE[2024-04-17 07:10:56.353][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:56.354][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:56.355][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.356][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.360][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.361][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.362][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.364][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.365][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.366][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.367][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.368][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.369][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.370][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:56.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.382][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-17 07:10:56.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:56.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.403][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.405][private$selectFields]
biodb.TRACE[2024-04-17 07:10:56.406][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:10:56.407][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:10:56.408][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.412][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.413][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.415][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.424][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.426][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.427][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-17 07:10:56.428][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.429][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.431][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.432][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-17 07:10:56.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.444][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-04-17 07:10:56.445][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:10:56.446][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-17 07:10:56.467][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-17 07:10:56.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-17 07:10:56.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:56.475][biodb::testThat]
biodb.INFO [2024-04-17 07:10:56.475][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-04-17 07:10:56.476][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:56.477][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:56.479][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-04-17 07:10:56.480][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:56.481][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-04-17 07:10:56.483][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:56.486][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2024-04-17 07:10:56.487][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:56.488][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:56.489][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:56.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:56.506][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.507][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.509][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.513][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:56.514][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:56.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.516][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.517][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:56.518][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:56.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.520][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.521][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:56.522][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:56.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.523][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.524][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.525][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.527][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.528][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.529][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.530][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.531][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:56.532][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:56.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.534][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.535][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.536][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.538][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.539][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:56.541][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:56.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.543][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.545][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:56.546][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:56.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.547][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.548][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:56.549][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:56.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.551][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:56.598][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-04-17 07:10:56.599][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-04-17 07:10:56.608][biodb::testThat]
biodb.INFO [2024-04-17 07:10:56.609][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-04-17 07:10:56.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:56.612][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:56.624][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-04-17 07:10:56.625][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-04-17 07:10:56.626][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-04-17 07:10:56.628][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-04-17 07:10:56.629][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-04-17 07:10:56.632][loadFileContents] Loaded 3 files from cache: [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2024-04-17 07:10:56.633][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:56.634][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-04-17 07:10:56.635][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:56.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:56.655][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.657][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.659][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.664][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:56.665][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:56.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.666][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.668][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:56.669][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:56.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.670][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.671][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:56.672][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:56.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.674][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.675][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.676][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.677][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.678][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.679][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.681][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.682][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:56.683][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:56.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.684][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.685][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.686][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.688][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.689][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:56.689][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:56.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.691][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.692][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:56.693][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:56.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.694][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.695][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:56.696][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:56.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.698][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:56.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.736][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[2024-04-17 07:10:56.739][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.740][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.741][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.746][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:56.747][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:56.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.748][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.749][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:56.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:56.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.753][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:56.762][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:56.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.764][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:56.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:56.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.770][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:56.771][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:56.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.772][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:56.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:56.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.780][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.783][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.788][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.789][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.791][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.792][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.795][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:56.796][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:56.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.798][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.799][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:56.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:56.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.803][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.805][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.807][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.813][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:56.814][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:56.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.815][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:56.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:56.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.821][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:56.822][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:56.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.823][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.824][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:56.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:56.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.828][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:56.829][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:56.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.830][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.832][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:56.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:56.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:56.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:56.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:56.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:56.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:56.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:56.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:56.875][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.TRACE[2024-04-17 07:10:56.877][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.878][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.880][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.885][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:56.885][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:56.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.887][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.888][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:56.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:56.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.891][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:56.892][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:56.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.894][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:56.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:56.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.898][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:56.899][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:56.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.901][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:56.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:56.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.905][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.906][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.908][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:56.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.913][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.922][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.924][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.926][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:56.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.932][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:56.934][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:56.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.935][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.936][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:56.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:56.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.940][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.941][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.942][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:56.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.947][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:56.948][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:56.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.949][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:56.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:56.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.954][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:56.955][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:56.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.957][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.958][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:56.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:56.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.961][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:56.962][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:56.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.964][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.965][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:56.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:56.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:56.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:56.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:56.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:56.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:56.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:57.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:57.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:57.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:57.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:57.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:57.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:57.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:57.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:57.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:57.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:57.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:57.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:57.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:57.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:57.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:57.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:57.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:57.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:57.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:57.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:57.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:57.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:57.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:57.028][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-04-17 07:10:57.030][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-04-17 07:10:57.031][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-04-17 07:10:57.045][biodb::testThat]
biodb.INFO [2024-04-17 07:10:57.047][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-04-17 07:10:57.048][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:57.048][biodb::testThat]
biodb.INFO [2024-04-17 07:10:57.085][biodb::testThat]
biodb.INFO [2024-04-17 07:10:57.086][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-04-17 07:10:57.088][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:57.089][biodb::testThat]
biodb.INFO [2024-04-17 07:10:57.098][biodb::testThat]
biodb.INFO [2024-04-17 07:10:57.100][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-04-17 07:10:57.100][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:57.101][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:57.104][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[2024-04-17 07:10:57.107][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:57.109][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2024-04-17 07:10:57.110][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:57.113][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2024-04-17 07:10:57.126][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:57.128][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:57.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.129][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:57.130][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:57.131][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:57.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:57.133][ef$get] fields variable is a list.
biodb.INFO [2024-04-17 07:10:57.134][biodb::testThat]
biodb.INFO [2024-04-17 07:10:57.135][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-04-17 07:10:57.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:57.137][biodb::testThat]
biodb.ERROR[2024-04-17 07:10:57.151][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-04-17 07:10:57.171][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-04-17 07:10:57.186][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-17 07:10:57.188][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-04-17 07:10:57.189][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-04-17 07:10:57.190][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-17 07:10:57.192][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.193][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.195][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-17 07:10:57.208][biodb::testContext]
biodb.INFO [2024-04-17 07:10:57.210][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:10:57.211][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-04-17 07:10:57.212][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:10:57.213][biodb::testContext]
biodb.INFO [2024-04-17 07:10:57.215][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:10:57.217][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-17 07:10:57.222][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:57.223][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-17 07:10:57.224][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-17 07:10:57.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.228][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-17 07:10:57.245][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-17 07:10:57.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.250][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-17 07:10:57.251][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-17 07:10:57.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.254][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-17 07:10:57.491][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-17 07:10:57.493][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-17 07:10:57.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.496][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-17 07:10:57.497][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-17 07:10:57.498][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-17 07:10:57.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.500][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-17 07:10:57.501][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-17 07:10:57.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.505][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-17 07:10:57.507][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-17 07:10:57.508][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-17 07:10:57.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.511][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-17 07:10:57.512][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-17 07:10:57.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.514][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[2024-04-17 07:10:57.515][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-17 07:10:57.516][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-17 07:10:57.516][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-17 07:10:57.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.519][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:10:57.520][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-17 07:10:57.521][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-17 07:10:57.522][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-17 07:10:57.522][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-17 07:10:57.523][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-17 07:10:57.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.526][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-17 07:10:57.527][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-17 07:10:57.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.530][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-17 07:10:57.531][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-17 07:10:57.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.535][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-17 07:10:57.537][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-17 07:10:57.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.540][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-17 07:10:57.541][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-17 07:10:57.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.544][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-17 07:10:57.545][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-17 07:10:57.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.548][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:10:57.549][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-17 07:10:57.571][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-17 07:10:57.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.575][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-17 07:10:57.576][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-17 07:10:57.576][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-17 07:10:57.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.579][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-17 07:10:57.581][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.582][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-17 07:10:57.583][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.584][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:57.584][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.585][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.586][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.587][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.588][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:10:57.588][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:57.590][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.591][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-17 07:10:57.592][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:57.593][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.595][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.595][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:57.595][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:57.595][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:57.595][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:10:57.595][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:10:57.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:57.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:57.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:57.599][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:57.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:57.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:57.601][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.602][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.603][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:57.604][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:57.604][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.605][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.606][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-17 07:10:57.608][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.609][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:10:57.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:57.611][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.612][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.613][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.615][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:10:57.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:57.616][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.617][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-17 07:10:57.618][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:57.619][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.621][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:57.621][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:57.621][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:57.621][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:10:57.621][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:10:57.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:57.622][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:57.623][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:57.624][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:57.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:57.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:57.626][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.627][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.629][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:57.630][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:57.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.632][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.633][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-17 07:10:57.635][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.636][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-17 07:10:57.637][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.638][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:57.639][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.640][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.641][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.642][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:10:57.643][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:57.644][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.645][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-17 07:10:57.646][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:57.647][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.647][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.648][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.649][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:57.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:57.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:57.654][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:57.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:57.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:57.657][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.658][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.659][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:57.660][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:57.661][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.662][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.663][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-17 07:10:57.665][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.666][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:10:57.667][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.668][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:57.669][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.670][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.671][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.672][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.672][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:10:57.673][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:57.674][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.675][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-17 07:10:57.676][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:57.677][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.678][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.679][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.680][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:57.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:57.681][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:57.682][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:57.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:57.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:57.685][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.686][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.687][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:57.688][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:57.690][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.691][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:57.694][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:57.695][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.700][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[2024-04-17 07:10:57.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.713][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[2024-04-17 07:10:57.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.721][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[2024-04-17 07:10:57.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.756][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[2024-04-17 07:10:57.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.760][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[2024-04-17 07:10:57.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.774][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-17 07:10:57.775][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-17 07:10:57.777][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-17 07:10:57.778][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-17 07:10:57.779][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:10:57.781][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-17 07:10:57.782][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-17 07:10:57.783][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-17 07:10:57.785][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-17 07:10:57.786][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-17 07:10:57.787][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:10:57.789][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-17 07:10:57.790][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-17 07:10:57.791][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-17 07:10:57.792][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-17 07:10:57.795][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:10:57.797][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-17 07:10:57.799][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-17 07:10:57.800][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:10:57.808][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-17 07:10:57.810][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-17 07:10:57.811][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-17 07:10:57.812][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-17 07:10:57.813][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-17 07:10:57.815][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-17 07:10:57.816][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-17 07:10:57.817][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-17 07:10:57.818][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-17 07:10:57.819][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-17 07:10:57.820][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-17 07:10:57.822][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-17 07:10:57.823][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-17 07:10:57.824][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-17 07:10:57.825][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-17 07:10:57.826][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-17 07:10:57.827][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-17 07:10:57.828][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-17 07:10:57.829][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-17 07:10:57.831][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-17 07:10:57.833][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-17 07:10:57.835][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-17 07:10:57.837][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-17 07:10:57.838][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-17 07:10:57.839][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-17 07:10:57.840][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-17 07:10:57.842][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-17 07:10:57.843][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-17 07:10:57.844][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-17 07:10:57.845][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-17 07:10:57.846][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-17 07:10:57.847][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-17 07:10:57.848][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-17 07:10:57.850][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-17 07:10:57.851][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-17 07:10:57.852][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-17 07:10:57.853][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-17 07:10:57.854][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-17 07:10:57.855][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-17 07:10:57.856][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-17 07:10:57.857][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-17 07:10:57.859][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-17 07:10:57.860][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-17 07:10:57.861][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-17 07:10:57.862][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-17 07:10:57.863][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-17 07:10:57.864][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-17 07:10:57.865][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:10:57.867][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:10:57.868][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-17 07:10:57.869][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-17 07:10:57.870][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-17 07:10:57.871][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-17 07:10:57.872][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-17 07:10:57.874][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-17 07:10:57.876][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-17 07:10:57.878][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-17 07:10:57.880][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-17 07:10:57.881][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-17 07:10:57.883][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-17 07:10:57.884][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-17 07:10:57.886][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-17 07:10:57.887][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-17 07:10:57.888][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-17 07:10:57.890][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-17 07:10:57.891][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:10:57.892][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:57.893][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.895][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.895][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.DEBUG[2024-04-17 07:10:57.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.911][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[2024-04-17 07:10:57.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.916][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[2024-04-17 07:10:57.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.921][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[2024-04-17 07:10:57.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.928][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[2024-04-17 07:10:57.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.934][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[2024-04-17 07:10:57.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.939][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[2024-04-17 07:10:57.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.944][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[2024-04-17 07:10:57.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.972][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.DEBUG[2024-04-17 07:10:57.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:57.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:57.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:57.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:57.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:57.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:57.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:57.989][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-04-17 07:10:57.991][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-04-17 07:10:57.993][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:57.994][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.995][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.996][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:57.996][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.997][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:57.998][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:57.999][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-04-17 07:10:58.000][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-04-17 07:10:58.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:58.002][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.003][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-04-17 07:10:58.004][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-04-17 07:10:58.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-04-17 07:10:58.007][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.008][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:58.008][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:58.008][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:58.009][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-17 07:10:58.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:58.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.015][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:58.015][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-04-17 07:10:58.016][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:58.016][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:58.017][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.018][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-04-17 07:10:58.018][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-04-17 07:10:58.019][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:10:58.021][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:10:58.022][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-04-17 07:10:58.023][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:10:58.025][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:10:58.026][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:10:58.029][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-04-17 07:10:58.030][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-04-17 07:10:58.031][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-04-17 07:10:58.032][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-04-17 07:10:58.034][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-17 07:10:58.034][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-17 07:10:58.035][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-04-17 07:10:58.036][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-04-17 07:10:58.038][biodb::testThat]
biodb.INFO [2024-04-17 07:10:58.039][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-04-17 07:10:58.039][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:58.040][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:58.044][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-04-17 07:10:58.047][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.049][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-04-17 07:10:58.050][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.052][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-04-17 07:10:58.057][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[2024-04-17 07:10:58.061][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.062][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-04-17 07:10:58.063][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.066][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-04-17 07:10:58.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.080][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[2024-04-17 07:10:58.083][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-04-17 07:10:58.086][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.088][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-04-17 07:10:58.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.133][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[2024-04-17 07:10:58.138][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[2024-04-17 07:10:58.142][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.143][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-04-17 07:10:58.144][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.145][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-04-17 07:10:58.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.157][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[2024-04-17 07:10:58.159][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[2024-04-17 07:10:58.164][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.165][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-04-17 07:10:58.166][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.167][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-04-17 07:10:58.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.179][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.DEBUG[2024-04-17 07:10:58.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.190][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[2024-04-17 07:10:58.194][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[2024-04-17 07:10:58.197][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.198][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-04-17 07:10:58.200][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.201][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-04-17 07:10:58.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.214][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[2024-04-17 07:10:58.216][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[2024-04-17 07:10:58.219][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.221][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-04-17 07:10:58.222][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.223][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-04-17 07:10:58.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.236][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[2024-04-17 07:10:58.240][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.241][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-04-17 07:10:58.242][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.245][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-04-17 07:10:58.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.258][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.INFO [2024-04-17 07:10:58.267][biodb::testThat]
biodb.INFO [2024-04-17 07:10:58.268][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-04-17 07:10:58.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:58.270][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:58.274][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[2024-04-17 07:10:58.278][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.280][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2024-04-17 07:10:58.281][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.283][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2024-04-17 07:10:58.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.300][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[2024-04-17 07:10:58.303][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.306][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2024-04-17 07:10:58.308][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.310][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2024-04-17 07:10:58.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:58.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-17 07:10:58.329][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-17 07:10:58.330][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-04-17 07:10:58.331][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-04-17 07:10:58.332][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-17 07:10:58.333][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.334][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.336][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-17 07:10:58.340][biodb::testContext]
biodb.INFO [2024-04-17 07:10:58.341][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:10:58.342][biodb::testContext] Test context - Test web services
biodb.INFO [2024-04-17 07:10:58.343][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:10:58.343][biodb::testContext]
biodb.INFO [2024-04-17 07:10:58.346][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:10:58.347][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-17 07:10:58.353][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:58.354][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-17 07:10:58.355][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-17 07:10:58.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.359][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-17 07:10:58.360][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-17 07:10:58.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.362][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[2024-04-17 07:10:58.363][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-17 07:10:58.364][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-17 07:10:58.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.367][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-17 07:10:58.368][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-17 07:10:58.368][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-17 07:10:58.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.371][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[2024-04-17 07:10:58.372][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-17 07:10:58.372][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-17 07:10:58.373][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-17 07:10:58.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.377][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-17 07:10:58.377][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-17 07:10:58.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.380][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-17 07:10:58.381][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-17 07:10:58.382][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-17 07:10:58.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.385][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-17 07:10:58.386][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-17 07:10:58.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.389][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-17 07:10:58.391][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-17 07:10:58.392][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-17 07:10:58.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.398][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:10:58.400][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-17 07:10:58.401][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-17 07:10:58.402][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-17 07:10:58.403][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-17 07:10:58.404][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-17 07:10:58.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.407][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-17 07:10:58.408][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-17 07:10:58.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.411][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-17 07:10:58.412][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-17 07:10:58.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.415][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-17 07:10:58.416][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-17 07:10:58.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.418][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-17 07:10:58.419][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-17 07:10:58.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.423][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-17 07:10:58.424][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-17 07:10:58.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.428][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:10:58.429][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-17 07:10:58.450][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-17 07:10:58.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.462][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-17 07:10:58.463][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-17 07:10:58.464][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-17 07:10:58.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.467][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-17 07:10:58.469][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.470][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-17 07:10:58.471][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.472][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:58.472][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.473][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.474][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.475][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.476][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:10:58.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:58.477][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.478][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-17 07:10:58.479][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:58.480][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.481][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.483][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:58.483][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:58.483][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:58.483][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:10:58.483][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:10:58.484][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:58.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.486][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.487][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:58.489][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.490][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.492][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:58.494][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:58.495][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.496][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.497][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-17 07:10:58.499][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.500][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:10:58.500][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.501][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:58.502][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.503][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.504][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.504][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.505][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:10:58.508][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:58.509][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.510][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-17 07:10:58.511][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:58.511][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.512][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.513][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:58.513][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:58.513][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:58.513][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:10:58.513][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:10:58.514][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:58.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.518][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:58.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.521][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.522][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:58.523][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:58.524][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.525][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.526][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-17 07:10:58.529][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.530][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-17 07:10:58.531][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:58.533][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.534][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.535][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.536][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:10:58.537][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:58.538][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.539][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-17 07:10:58.540][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:58.541][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.541][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.542][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.543][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:58.544][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.545][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:58.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.548][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.549][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.549][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:58.550][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:58.551][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.552][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.553][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-17 07:10:58.554][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.555][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:10:58.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.557][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:58.558][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.559][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.559][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.560][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.561][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:10:58.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:58.563][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.563][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-17 07:10:58.564][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:58.565][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.566][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.567][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.567][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:58.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.571][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:58.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.576][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.576][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:58.577][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:58.578][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.579][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:58.580][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:58.581][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.628][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[2024-04-17 07:10:58.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.647][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.DEBUG[2024-04-17 07:10:58.648][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-17 07:10:58.649][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-17 07:10:58.651][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-17 07:10:58.652][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-17 07:10:58.653][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:10:58.654][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-17 07:10:58.656][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-17 07:10:58.657][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-17 07:10:58.658][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-17 07:10:58.659][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-17 07:10:58.661][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:10:58.662][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-17 07:10:58.663][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-17 07:10:58.664][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-17 07:10:58.665][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-17 07:10:58.667][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:10:58.668][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-17 07:10:58.669][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-17 07:10:58.670][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:10:58.671][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-17 07:10:58.672][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-17 07:10:58.673][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-17 07:10:58.675][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-17 07:10:58.676][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-17 07:10:58.677][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-17 07:10:58.679][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-17 07:10:58.681][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-17 07:10:58.684][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-17 07:10:58.686][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-17 07:10:58.688][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-17 07:10:58.690][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-17 07:10:58.692][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-17 07:10:58.693][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-17 07:10:58.695][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-17 07:10:58.696][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-17 07:10:58.697][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-17 07:10:58.698][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-17 07:10:58.699][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-17 07:10:58.701][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-17 07:10:58.702][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-17 07:10:58.703][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-17 07:10:58.704][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-17 07:10:58.705][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-17 07:10:58.707][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-17 07:10:58.708][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-17 07:10:58.709][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-17 07:10:58.710][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-17 07:10:58.711][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-17 07:10:58.712][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-17 07:10:58.714][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-17 07:10:58.715][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-17 07:10:58.716][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-17 07:10:58.717][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-17 07:10:58.718][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-17 07:10:58.719][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-17 07:10:58.720][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-17 07:10:58.722][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-17 07:10:58.723][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-17 07:10:58.724][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-17 07:10:58.725][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-17 07:10:58.726][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-17 07:10:58.727][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-17 07:10:58.729][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-17 07:10:58.737][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-17 07:10:58.739][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-17 07:10:58.740][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-17 07:10:58.741][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:10:58.742][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:10:58.743][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-17 07:10:58.745][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-17 07:10:58.746][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-17 07:10:58.747][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-17 07:10:58.748][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-17 07:10:58.749][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-17 07:10:58.750][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-17 07:10:58.751][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-17 07:10:58.752][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-17 07:10:58.754][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-17 07:10:58.755][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-17 07:10:58.756][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-17 07:10:58.757][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-17 07:10:58.759][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-17 07:10:58.761][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-17 07:10:58.762][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-17 07:10:58.764][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:10:58.766][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:58.768][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.769][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.786][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[2024-04-17 07:10:58.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.811][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[2024-04-17 07:10:58.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.817][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[2024-04-17 07:10:58.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.852][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.DEBUG[2024-04-17 07:10:58.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.866][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-04-17 07:10:58.868][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-04-17 07:10:58.870][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.871][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.872][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.872][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:58.873][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.874][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.875][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.876][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-04-17 07:10:58.876][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-04-17 07:10:58.877][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:58.878][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.880][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-04-17 07:10:58.881][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-04-17 07:10:58.883][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-04-17 07:10:58.884][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:58.885][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:58.885][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:58.885][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:58.886][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-17 07:10:58.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.888][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:58.889][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:58.890][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:58.890][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:58.891][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:58.891][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-04-17 07:10:58.892][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:58.893][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:58.894][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:58.894][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-04-17 07:10:58.894][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-04-17 07:10:58.896][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:10:58.897][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:10:58.898][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-04-17 07:10:58.900][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:10:58.901][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:10:58.902][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:10:58.906][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-04-17 07:10:58.907][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-04-17 07:10:58.908][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-04-17 07:10:58.909][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-04-17 07:10:58.911][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-17 07:10:58.912][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-17 07:10:58.914][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-04-17 07:10:58.915][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-04-17 07:10:58.916][biodb::testThat]
biodb.INFO [2024-04-17 07:10:58.917][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-04-17 07:10:58.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:58.919][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:58.922][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-04-17 07:10:58.928][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-04-17 07:10:58.931][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.932][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-04-17 07:10:58.936][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[2024-04-17 07:10:58.939][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:58.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-04-17 07:10:58.942][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:58.943][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2024-04-17 07:10:58.952][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-17 07:10:58.953][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-04-17 07:10:58.955][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-04-17 07:10:58.955][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-17 07:10:58.956][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:58.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:58.958][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:58.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:58.959][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.960][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.INFO [2024-04-17 07:10:58.965][biodb::testContext]
biodb.INFO [2024-04-17 07:10:58.966][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:10:58.967][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-04-17 07:10:58.967][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:10:58.968][biodb::testContext]
biodb.INFO [2024-04-17 07:10:58.971][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:10:58.973][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-17 07:10:58.978][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:58.979][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-17 07:10:58.980][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-17 07:10:58.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.983][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-17 07:10:58.984][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-17 07:10:58.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.988][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-17 07:10:58.989][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-17 07:10:58.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.992][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-17 07:10:58.993][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-17 07:10:58.994][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-17 07:10:58.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:58.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:58.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:58.997][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-17 07:10:58.998][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-17 07:10:58.998][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-17 07:10:59.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.004][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-17 07:10:59.005][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-17 07:10:59.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.009][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-17 07:10:59.009][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-17 07:10:59.010][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-17 07:10:59.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.013][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-17 07:10:59.014][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-17 07:10:59.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.017][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-17 07:10:59.018][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-17 07:10:59.019][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-17 07:10:59.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.022][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:10:59.023][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-17 07:10:59.023][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-17 07:10:59.024][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-17 07:10:59.025][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-17 07:10:59.032][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-17 07:10:59.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.036][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-17 07:10:59.037][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-17 07:10:59.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.040][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-17 07:10:59.040][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-17 07:10:59.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.045][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-17 07:10:59.046][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-17 07:10:59.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.049][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-17 07:10:59.050][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-17 07:10:59.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.052][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[2024-04-17 07:10:59.053][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-17 07:10:59.054][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-17 07:10:59.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.057][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:10:59.058][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-17 07:10:59.079][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-17 07:10:59.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.084][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-17 07:10:59.085][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-17 07:10:59.086][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-17 07:10:59.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.089][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-17 07:10:59.091][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.092][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-17 07:10:59.093][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.094][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:59.094][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.095][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.096][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.097][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.098][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:10:59.098][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:59.099][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.100][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-17 07:10:59.101][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:59.102][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.103][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.104][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:59.104][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:59.104][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:59.104][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:10:59.104][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:10:59.105][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:59.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.107][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:59.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.110][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.111][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.111][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:59.112][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:59.113][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.114][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.115][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-17 07:10:59.117][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.118][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:10:59.119][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.120][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:59.120][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.121][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.122][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.123][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.123][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:10:59.124][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:59.125][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.126][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-17 07:10:59.127][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:59.128][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.128][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.129][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:59.129][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:59.129][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:59.129][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:10:59.129][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:10:59.130][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:59.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.133][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:59.133][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.135][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.136][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.136][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:59.137][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:59.138][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.139][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.140][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-17 07:10:59.141][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.142][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-17 07:10:59.143][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.144][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:59.145][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.145][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.146][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.147][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.148][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:10:59.148][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:59.149][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.150][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-17 07:10:59.151][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:59.152][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.152][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.153][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.154][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:59.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.157][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:59.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.159][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.160][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.161][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:59.161][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:59.162][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.163][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.164][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-17 07:10:59.165][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.166][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:10:59.167][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:59.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.170][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.171][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.172][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:10:59.173][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:59.174][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.174][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-17 07:10:59.175][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:59.176][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.177][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.178][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.178][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:10:59.179][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.180][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.181][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:59.181][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.182][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.183][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.185][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.186][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:59.187][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:59.188][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.189][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:10:59.190][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:59.190][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.191][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[2024-04-17 07:10:59.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.195][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[2024-04-17 07:10:59.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.198][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[2024-04-17 07:10:59.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.209][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[2024-04-17 07:10:59.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.213][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.DEBUG[2024-04-17 07:10:59.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.227][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[2024-04-17 07:10:59.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.254][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-17 07:10:59.256][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-17 07:10:59.258][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-17 07:10:59.259][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-17 07:10:59.260][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:10:59.262][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-17 07:10:59.263][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-17 07:10:59.264][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-17 07:10:59.265][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-17 07:10:59.266][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-17 07:10:59.267][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:10:59.269][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-17 07:10:59.271][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-17 07:10:59.272][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-17 07:10:59.273][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-17 07:10:59.274][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:10:59.276][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-17 07:10:59.278][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-17 07:10:59.279][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:10:59.280][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-17 07:10:59.282][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-17 07:10:59.283][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-17 07:10:59.284][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-17 07:10:59.285][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-17 07:10:59.286][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-17 07:10:59.288][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-17 07:10:59.290][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-17 07:10:59.291][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-17 07:10:59.292][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-17 07:10:59.293][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-17 07:10:59.295][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-17 07:10:59.296][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-17 07:10:59.297][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-17 07:10:59.298][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-17 07:10:59.299][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-17 07:10:59.301][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-17 07:10:59.302][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-17 07:10:59.303][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-17 07:10:59.304][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-17 07:10:59.305][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-17 07:10:59.313][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-17 07:10:59.314][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-17 07:10:59.316][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-17 07:10:59.317][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-17 07:10:59.318][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-17 07:10:59.319][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-17 07:10:59.320][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-17 07:10:59.321][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-17 07:10:59.323][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-17 07:10:59.324][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-17 07:10:59.325][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-17 07:10:59.327][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-17 07:10:59.328][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-17 07:10:59.329][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-17 07:10:59.330][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-17 07:10:59.331][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-17 07:10:59.332][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-17 07:10:59.333][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-17 07:10:59.335][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-17 07:10:59.336][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-17 07:10:59.337][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-17 07:10:59.338][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-17 07:10:59.339][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-17 07:10:59.340][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-17 07:10:59.341][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-17 07:10:59.343][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-17 07:10:59.344][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:10:59.345][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:10:59.346][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-17 07:10:59.347][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-17 07:10:59.348][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-17 07:10:59.349][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-17 07:10:59.350][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-17 07:10:59.352][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-17 07:10:59.353][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-17 07:10:59.354][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-17 07:10:59.355][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-17 07:10:59.356][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-17 07:10:59.357][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-17 07:10:59.358][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-17 07:10:59.359][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-17 07:10:59.360][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-17 07:10:59.362][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-17 07:10:59.363][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-17 07:10:59.365][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:10:59.366][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:10:59.366][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.368][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.385][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[2024-04-17 07:10:59.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.390][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.DEBUG[2024-04-17 07:10:59.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.455][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.DEBUG[2024-04-17 07:10:59.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:10:59.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:10:59.462][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-04-17 07:10:59.464][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-04-17 07:10:59.466][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.467][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.467][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.468][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:10:59.469][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.470][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.471][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.471][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-04-17 07:10:59.472][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-04-17 07:10:59.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:10:59.474][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.475][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-04-17 07:10:59.475][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-04-17 07:10:59.476][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-04-17 07:10:59.477][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-17 07:10:59.478][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:10:59.478][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:10:59.478][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:10:59.479][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-17 07:10:59.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.484][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:10:59.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:10:59.485][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:10:59.486][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:10:59.487][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-17 07:10:59.487][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-04-17 07:10:59.488][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:10:59.489][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:10:59.489][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-17 07:10:59.490][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-04-17 07:10:59.490][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-04-17 07:10:59.491][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:10:59.493][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:10:59.494][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-04-17 07:10:59.496][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:10:59.497][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:10:59.498][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:10:59.501][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-04-17 07:10:59.502][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-04-17 07:10:59.504][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-04-17 07:10:59.505][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-04-17 07:10:59.506][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-17 07:10:59.507][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-17 07:10:59.508][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-04-17 07:10:59.509][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-04-17 07:10:59.510][biodb::testThat]
biodb.INFO [2024-04-17 07:10:59.511][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-04-17 07:10:59.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:10:59.513][biodb::testThat]
biodb.DEBUG[2024-04-17 07:10:59.516][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-04-17 07:10:59.521][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:59.522][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-04-17 07:10:59.524][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:59.525][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-04-17 07:10:59.529][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[2024-04-17 07:10:59.532][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:10:59.534][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-04-17 07:10:59.535][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:59.536][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-04-17 07:10:59.542][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-04-17 07:10:59.543][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:10:59.544][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-04-17 07:10:59.545][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:10:59.548][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2024-04-17 07:10:59.549][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:10:59.550][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:10:59.552][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-17 07:10:59.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:10:59.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:10:59.569][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:59.570][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:59.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.572][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:59.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:59.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.577][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:59.577][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:59.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.579][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.580][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-17 07:10:59.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-17 07:10:59.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.584][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:59.585][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:59.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.586][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.595][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:10:59.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:10:59.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.600][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-17 07:10:59.601][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-17 07:10:59.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.604][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.605][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-17 07:10:59.606][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-17 07:10:59.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.608][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.609][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:59.610][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:59.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.612][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.613][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:59.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:10:59.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.616][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:59.617][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:59.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.619][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.620][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-17 07:10:59.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:10:59.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.624][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:59.625][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:59.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.626][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:59.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:10:59.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.631][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:59.632][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:59.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.633][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:10:59.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:10:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.639][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:59.640][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:59.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.641][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.643][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-17 07:10:59.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-17 07:10:59.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.649][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:59.650][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:59.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.651][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.653][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-17 07:10:59.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-17 07:10:59.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:59.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:59.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:59.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:59.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:59.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:59.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:10:59.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:10:59.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:59.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:59.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:59.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:59.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:59.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:59.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:59.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:59.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:59.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:59.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:10:59.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:10:59.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:10:59.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:10:59.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:10:59.692][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-04-17 07:10:59.696][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-17 07:10:59.698][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-04-17 07:10:59.699][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-04-17 07:10:59.699][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-17 07:10:59.700][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:10:59.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:10:59.702][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:10:59.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:10:59.703][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:10:59.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 378 ]
> 
> proc.time()
   user  system elapsed 
 16.724   0.954  22.018

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.7160.8774.429
ChebiEntry0.3550.0180.383