Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:37 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for biodbChebi on merida1


To the developers/maintainers of the biodbChebi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 177/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.2.0  (landing page)
Pierrick Roger
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_15
git_last_commit: 24c8926
git_last_commit_date: 2022-04-26 12:18:32 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biodbChebi
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2022-10-18 23:48:31 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 23:51:20 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 169.6 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/biodbChebi.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.2.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 4.547  0.715   6.195
* 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/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 [2022-10-18 23:49:50.833][biodb::testContext]
biodb.INFO [2022-10-18 23:49:50.851][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:49:50.853][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-10-18 23:49:50.855][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:49:50.857][biodb::testContext]
biodb.INFO [2022-10-18 23:49:50.888][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:49:50.891][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 23:49:50.905][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:49:50.906][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 23:49:50.908][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 23:49:50.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:50.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:50.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:50.916][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 23:49:50.957][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 23:49:50.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:50.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:50.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:50.963][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 23:49:50.966][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 23:49:50.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:50.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:50.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:50.973][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 23:49:50.976][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 23:49:50.978][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 23:49:50.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:50.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:50.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:50.985][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 23:49:50.987][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 23:49:50.988][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 23:49:50.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:50.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:50.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:50.995][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 23:49:50.998][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 23:49:50.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.005][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 23:49:51.006][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 23:49:51.009][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 23:49:51.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.016][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 23:49:51.018][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 23:49:51.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.024][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[2022-10-18 23:49:51.026][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 23:49:51.028][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 23:49:51.030][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 23:49:51.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.038][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:49:51.040][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 23:49:51.042][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 23:49:51.044][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 23:49:51.046][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 23:49:51.048][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 23:49:51.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.055][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 23:49:51.057][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 23:49:51.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.064][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 23:49:51.066][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 23:49:51.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.073][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 23:49:51.075][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 23:49:51.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.083][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 23:49:51.086][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 23:49:51.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.093][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 23:49:51.096][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 23:49:51.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.104][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:49:51.107][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 23:49:51.122][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-10-18 23:49:51.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.130][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 23:49:51.132][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 23:49:51.134][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 23:49:51.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.148][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 23:49:51.239][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.276][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 23:49:51.278][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.280][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:49:51.283][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.285][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.287][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.290][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.292][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:49:51.294][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:49:51.296][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.299][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 23:49:51.301][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:49:51.303][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.305][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.307][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:49:51.307][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:49:51.307][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:49:51.307][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:49:51.307][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:49:51.310][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:49:51.312][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:51.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:51.316][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:49:51.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:51.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:51.322][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.325][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.327][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:49:51.329][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:49:51.331][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.333][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.336][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 23:49:51.339][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.342][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:49:51.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.347][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:49:51.348][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.350][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.352][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.354][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.356][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:49:51.358][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:49:51.360][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.363][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 23:49:51.366][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:49:51.368][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.370][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.372][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:49:51.372][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:49:51.372][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:49:51.372][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:49:51.372][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:49:51.375][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:49:51.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:51.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:51.381][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:49:51.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:51.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:51.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.388][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.389][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:49:51.391][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:49:51.392][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.394][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.397][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 23:49:51.401][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.403][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 23:49:51.405][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.407][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:49:51.408][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.410][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.412][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.414][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.416][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:49:51.419][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:49:51.420][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.422][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 23:49:51.424][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:49:51.426][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.428][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.431][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.433][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:49:51.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:51.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:51.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:49:51.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:51.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:51.446][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.448][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:49:51.452][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:49:51.454][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.456][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.458][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 23:49:51.461][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.463][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:49:51.465][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.467][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:49:51.469][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.471][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.474][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.476][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.478][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:49:51.480][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:49:51.482][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.483][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 23:49:51.485][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:49:51.487][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.490][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:51.492][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.494][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:49:51.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:51.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:51.501][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:49:51.504][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:51.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:51.508][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:49:51.510][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:49:51.514][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:49:51.517][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:51.519][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:49:51.525][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:49:51.527][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.528][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[2022-10-18 23:49:51.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.582][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[2022-10-18 23:49:51.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.610][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[2022-10-18 23:49:51.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.639][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[2022-10-18 23:49:51.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.658][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[2022-10-18 23:49:51.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:51.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:51.700][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 23:49:51.710][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 23:49:51.713][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 23:49:51.717][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 23:49:51.720][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:49:51.723][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 23:49:51.727][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 23:49:51.730][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 23:49:51.733][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 23:49:51.736][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 23:49:51.739][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:49:51.743][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 23:49:51.746][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 23:49:51.749][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 23:49:51.752][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 23:49:51.755][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:49:51.757][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 23:49:51.761][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 23:49:51.764][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:49:51.767][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 23:49:51.770][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 23:49:51.772][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 23:49:51.775][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 23:49:51.777][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 23:49:51.780][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 23:49:51.783][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 23:49:51.786][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 23:49:51.789][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 23:49:51.792][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 23:49:51.795][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 23:49:51.799][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 23:49:51.801][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 23:49:51.805][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 23:49:51.808][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 23:49:51.810][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 23:49:51.813][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 23:49:51.816][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 23:49:51.819][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 23:49:51.821][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 23:49:51.824][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 23:49:51.826][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 23:49:51.829][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 23:49:51.832][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 23:49:51.835][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 23:49:51.839][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 23:49:51.842][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 23:49:51.846][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 23:49:51.849][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 23:49:51.852][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 23:49:51.855][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 23:49:51.859][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 23:49:51.862][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 23:49:51.865][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 23:49:51.878][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 23:49:51.881][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 23:49:51.884][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 23:49:51.888][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 23:49:51.891][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 23:49:51.894][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 23:49:51.898][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 23:49:51.901][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 23:49:51.904][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 23:49:51.907][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 23:49:51.909][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 23:49:51.911][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 23:49:51.913][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 23:49:51.915][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:49:51.918][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:49:51.922][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 23:49:51.925][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 23:49:51.927][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 23:49:51.929][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 23:49:51.931][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 23:49:51.933][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 23:49:51.936][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 23:49:51.939][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 23:49:51.942][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 23:49:51.945][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 23:49:51.949][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 23:49:51.952][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 23:49:51.956][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 23:49:51.959][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 23:49:51.962][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 23:49:51.973][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 23:49:51.977][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:49:51.984][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:49:51.986][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:51.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:51.990][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:51.992][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.DEBUG[2022-10-18 23:49:52.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.039][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[2022-10-18 23:49:52.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.052][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[2022-10-18 23:49:52.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.150][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.DEBUG[2022-10-18 23:49:52.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:49:52.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.237][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[2022-10-18 23:49:52.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:49:52.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.250][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[2022-10-18 23:49:52.253][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-10-18 23:49:52.275][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-10-18 23:49:52.279][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:52.281][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 23:49:52.283][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:52.286][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:49:52.288][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:52.290][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:49:52.292][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:52.294][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-10-18 23:49:52.296][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 23:49:52.299][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:49:52.301][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:52.303][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-10-18 23:49:52.306][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-10-18 23:49:52.308][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-10-18 23:49:52.310][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 23:49:52.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:49:52.313][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:49:52.313][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:49:52.315][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 23:49:52.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:52.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:52.321][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:49:52.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:49:52.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:49:52.327][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:49:52.329][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:49:52.329][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-10-18 23:49:52.331][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:49:52.333][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:49:52.335][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 23:49:52.337][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-10-18 23:49:52.337][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-10-18 23:49:52.351][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:49:52.354][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:49:52.357][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-10-18 23:49:52.361][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:49:52.364][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:49:52.367][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:49:52.417][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-10-18 23:49:52.419][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-10-18 23:49:52.429][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-10-18 23:49:52.438][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-10-18 23:49:52.448][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 23:49:52.450][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 23:49:52.452][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-10-18 23:49:52.454][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-10-18 23:49:52.488][biodb::testThat]
biodb.INFO [2022-10-18 23:49:52.490][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-10-18 23:49:52.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:49:52.494][biodb::testThat]
biodb.TRACE[2022-10-18 23:49:52.504][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2022-10-18 23:49:52.514][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:49:52.522][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:49:52.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:49:52.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:52.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:52.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:52.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:52.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:52.583][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[2022-10-18 23:49:52.618][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:52.621][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:52.623][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.625][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:52.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:52.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.673][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:52.676][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:52.678][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.680][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.748][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:52.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:52.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.763][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:52.765][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:52.767][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.769][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:52.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:52.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.785][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:52.788][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:52.790][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.792][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:52.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:52.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.810][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:52.812][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:52.815][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.817][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:52.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:52.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.833][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:52.836][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:52.838][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.840][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.843][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:52.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:52.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.858][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:49:52.860][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:52.862][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.864][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.867][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:49:52.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:52.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.891][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:52.893][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:52.895][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.897][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:52.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:52.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.914][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:52.916][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:52.919][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.921][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:52.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:52.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.939][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:49:52.942][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:52.944][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.946][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.949][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:49:52.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:52.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.964][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:52.967][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:52.969][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.971][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.973][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:52.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:52.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:52.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:52.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:52.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:52.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:49:53.184][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2022-10-18 23:49:53.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:53.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:53.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:53.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:53.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:53.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:53.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:53.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:53.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.317][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:49:53.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:49:53.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:49:53.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:49:53.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.336][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 23:49:53.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 23:49:53.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.344][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 23:49:53.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 23:49:53.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.560][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.562][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.564][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.566][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:53.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:53.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.627][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.630][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.633][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.635][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:53.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:53.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:53.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:53.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:53.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:53.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:53.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.694][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:53.697][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:53.699][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.701][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:53.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:53.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:53.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:53.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.741][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:53.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:53.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:53.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:53.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.757][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:53.758][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:53.760][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.762][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.764][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:53.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:53.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.812][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.814][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.816][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.818][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:53.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.867][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.870][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.873][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.875][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:53.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.903][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:53.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:53.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.912][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:53.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:53.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.921][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:53.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:53.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.930][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:53.932][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:53.934][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.936][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.939][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:53.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:53.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.972][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 23:49:53.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:53.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.981][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 23:49:53.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:53.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.990][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 23:49:53.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:53.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:53.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:53.999][ef$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 23:49:54.001][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:54.004][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.006][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.008][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 23:49:54.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:54.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.031][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.040][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.049][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.057][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.060][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.062][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.064][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.066][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.089][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:54.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:54.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.099][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:54.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:54.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.109][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:54.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:54.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.119][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:54.121][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:54.123][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.126][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:54.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:54.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.181][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.183][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.186][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.188][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:54.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:54.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:54.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:54.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:54.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:54.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.249][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:54.251][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:54.254][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.256][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:54.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.281][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:54.283][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:54.285][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.287][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.298][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:54.301][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:54.303][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.305][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.316][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:54.319][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:54.322][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.324][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.335][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:54.338][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:54.340][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.342][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.355][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.357][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.359][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.361][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.373][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.375][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.378][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.380][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.390][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:54.393][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:54.395][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.397][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.408][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:54.411][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:54.413][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.415][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.427][ef$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 23:49:54.429][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:54.432][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.434][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.446][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:54.449][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:54.451][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.453][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.465][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:54.468][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:54.470][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.472][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 23:49:54.485][biodb::testThat]
biodb.INFO [2022-10-18 23:49:54.487][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-10-18 23:49:54.489][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:49:54.491][biodb::testThat]
biodb.DEBUG[2022-10-18 23:49:54.534][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2022-10-18 23:49:54.552][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:49:54.559][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2022-10-18 23:49:54.562][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:49:54.565][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2022-10-18 23:49:54.568][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:49:54.670][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:49:54.673][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:49:54.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:49:54.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:49:54.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:49:54.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:49:54.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:49:54.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:49:54.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:49:54.702][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:54.705][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:54.707][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.710][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:54.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:54.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.779][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:54.782][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:54.784][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.786][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:49:54.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:49:54.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.804][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:54.806][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:54.808][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.810][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.813][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:49:54.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:49:54.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.829][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:54.831][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:54.833][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.835][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:54.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:54.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.852][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.854][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.856][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.859][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:54.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.877][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.879][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.881][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.883][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.886][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:49:54.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.901][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:49:54.904][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:54.906][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.908][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.910][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:49:54.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:54.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.925][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:54.927][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:54.929][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.931][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:54.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:54.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.949][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:54.951][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:54.953][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.955][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:54.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:54.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.973][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:49:54.975][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:54.977][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.979][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.982][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:49:54.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:49:54.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:54.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:54.997][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:55.000][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:55.002][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.004][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.007][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:49:55.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:49:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:55.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:55.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:55.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:55.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:55.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:55.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:49:55.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:49:55.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:55.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:55.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:55.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:55.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:55.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:55.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:55.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:55.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:55.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:55.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:49:55.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:49:55.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:49:55.129][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2022-10-18 23:49:55.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-18 23:49:55.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-18 23:49:55.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-18 23:49:55.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-18 23:49:55.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-18 23:49:55.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-18 23:49:55.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:49:55.169][biodb::testThat]
biodb.INFO [2022-10-18 23:49:55.172][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-10-18 23:49:55.174][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:49:55.176][biodb::testThat]
biodb.TRACE[2022-10-18 23:49:55.182][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:55.184][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:55.187][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.189][ef$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:49:55.191][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2022-10-18 23:49:55.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:55.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:55.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:55.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:55.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:55.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:55.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:55.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:55.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:49:55.283][function(conn, opt)] With value "squalene".
biodb.DEBUG[2022-10-18 23:49:55.310][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-10-18 23:49:55.362][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:49:55.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-10-18 23:49:55.403][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:49:55.406][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-10-18 23:49:55.463][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[2022-10-18 23:49:55.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:49:55.472][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:49:55.476][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:49:56.307][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:49:56.910][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:49:56.926][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2022-10-18 23:49:56.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2022-10-18 23:49:56.988][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2022-10-18 23:49:57.032][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:57.035][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:49:57.036][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.038][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.040][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.042][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.044][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.045][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 23:49:57.049][biodb::testThat]
biodb.INFO [2022-10-18 23:49:57.050][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-10-18 23:49:57.052][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:49:57.054][biodb::testThat]
biodb.TRACE[2022-10-18 23:49:57.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:57.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:57.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:57.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:57.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:49:57.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:49:57.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:49:57.314][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:49:57.320][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:49:57.322][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 23:49:57.325][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:49:57.327][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2022-10-18 23:49:57.356][biodb::testThat]
biodb.INFO [2022-10-18 23:49:57.358][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-10-18 23:49:57.360][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:49:57.362][biodb::testThat]
biodb.TRACE[2022-10-18 23:49:57.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:57.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:57.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:57.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:57.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:57.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:57.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:57.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:57.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.539][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:49:57.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:49:57.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:49:57.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:49:57.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.566][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 23:49:57.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 23:49:57.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.574][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 23:49:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 23:49:57.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:57.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:57.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:49:57.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:49:57.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:57.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:57.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:49:57.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:49:57.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:49:57.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.687][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:49:57.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:49:57.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.696][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 23:49:57.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 23:49:57.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.705][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 23:49:57.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 23:49:57.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:49:57.716][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 23:49:57.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 23:49:57.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:49:57.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:49:57.732][biodb::testThat]
biodb.INFO [2022-10-18 23:49:57.734][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-10-18 23:49:57.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:49:57.739][biodb::testThat]
biodb.INFO [2022-10-18 23:49:57.758][biodb::testThat]
biodb.INFO [2022-10-18 23:49:57.760][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-10-18 23:49:57.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:49:57.764][biodb::testThat]
biodb.INFO [2022-10-18 23:49:57.776][biodb::testThat]
biodb.INFO [2022-10-18 23:49:57.778][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-10-18 23:49:57.780][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:49:57.782][biodb::testThat]
biodb.DEBUG[2022-10-18 23:49:57.790][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2022-10-18 23:49:58.413][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2022-10-18 23:49:59.381][biodb::testThat]
biodb.INFO [2022-10-18 23:49:59.382][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-10-18 23:49:59.384][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:49:59.386][biodb::testThat]
biodb.DEBUG[2022-10-18 23:49:59.860][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[2022-10-18 23:50:00.325][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:00.327][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:00.329][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:00.331][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:00.332][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:00.334][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:00.336][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:00.337][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:00.341][biodb::testThat]
biodb.INFO [2022-10-18 23:50:00.343][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2022-10-18 23:50:00.345][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:00.347][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:00.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:00.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:00.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:00.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:00.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:00.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:00.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:00.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:00.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:00.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:00.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:00.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:00.776][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:00.784][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:00.787][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 23:50:00.790][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:00.793][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-10-18 23:50:00.966][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:00.973][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:00.976][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 23:50:00.979][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:00.982][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2022-10-18 23:50:01.017][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 23:50:01.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 23:50:01.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:01.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:01.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:01.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:01.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:01.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:01.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:01.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:01.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:01.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:01.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:01.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:01.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:01.189][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:01.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:01.232][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:01.275][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:01.733][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:02.241][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:02.257][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2022-10-18 23:50:02.284][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2022-10-18 23:50:02.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:02.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:02.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:02.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.319][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2022-10-18 23:50:02.436][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:02.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2022-10-18 23:50:02.442][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:02.444][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:02.447][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:02.449][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:02.450][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:02.452][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:02.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:02.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:02.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:02.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:02.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:02.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:02.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:02.479][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2022-10-18 23:50:02.485][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:02.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:02.489][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2022-10-18 23:50:02.931][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2022-10-18 23:50:03.416][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:03.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2022-10-18 23:50:03.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2022-10-18 23:50:03.477][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2022-10-18 23:50:03.485][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:03.520][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:03.523][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:03.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:03.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:03.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:03.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:03.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:03.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:03.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:03.550][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.552][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.554][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.556][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.573][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:03.575][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:03.576][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.579][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.581][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:03.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:03.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.596][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:03.599][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:03.601][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.603][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.607][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:03.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:03.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.622][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:03.624][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:03.626][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.629][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:03.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:03.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.646][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:03.648][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:03.651][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.653][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:03.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:03.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.670][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:03.673][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:03.675][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.677][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.680][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:03.682][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:03.684][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.686][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.689][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:03.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:03.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.704][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:03.707][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:03.709][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.711][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:03.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:03.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.729][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:03.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:03.733][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.736][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:03.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:03.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.753][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:03.755][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:03.758][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.760][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.763][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:03.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:03.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.778][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:03.779][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:03.781][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.783][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.785][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:03.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:03.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:03.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:03.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:03.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:03.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:03.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:03.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:03.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:03.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:03.895][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2022-10-18 23:50:03.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:03.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:03.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:03.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:03.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:03.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:03.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:03.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:03.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:03.941][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[2022-10-18 23:50:03.947][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:03.949][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:03.952][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:04.400][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:05.862][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:05.877][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2022-10-18 23:50:05.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2022-10-18 23:50:05.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:05.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:05.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:05.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:05.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:05.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:05.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:05.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:05.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:05.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:05.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:05.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:05.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:05.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:05.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:05.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:05.986][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:05.993][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:05.995][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:05.999][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:06.443][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:06.901][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:06.912][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2022-10-18 23:50:06.937][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2022-10-18 23:50:07.027][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[2022-10-18 23:50:07.035][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:07.037][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 23:50:07.039][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:07.042][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-10-18 23:50:07.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:07.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:07.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:07.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:07.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:07.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:07.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:07.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:07.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:07.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:07.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:07.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:07.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:07.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:07.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:07.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:07.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:07.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:07.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:07.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:07.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:07.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:07.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:07.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:07.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:07.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:07.143][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2022-10-18 23:50:07.145][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:07.149][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2022-10-18 23:50:07.151][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:07.153][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:07.155][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:07.157][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:07.159][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:07.161][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:07.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:07.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:07.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:07.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:07.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:07.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:07.230][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[2022-10-18 23:50:07.232][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2022-10-18 23:50:07.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:07.238][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:07.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2022-10-18 23:50:07.680][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2022-10-18 23:50:08.165][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:08.182][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2022-10-18 23:50:08.206][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2022-10-18 23:50:08.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2022-10-18 23:50:08.238][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:08.273][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:08.276][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:08.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:08.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:08.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:08.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:08.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:08.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:08.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:08.306][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:08.308][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:08.310][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.313][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:08.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:08.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.329][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:08.332][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:08.334][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.336][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.338][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:08.341][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:08.343][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.345][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.348][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:08.350][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:08.352][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.354][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.357][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:08.359][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:08.361][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.363][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.365][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:08.368][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:08.370][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.372][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.374][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:08.376][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.378][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.380][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.383][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:08.385][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:08.387][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.389][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.392][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:08.394][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:08.396][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.398][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:08.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:08.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.418][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:08.420][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:08.423][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.425][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.427][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:08.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:08.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.443][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:08.445][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:08.447][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.449][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:08.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:08.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:08.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:08.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:08.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:08.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:08.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:08.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:08.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:08.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:08.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:08.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:08.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:08.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:08.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:08.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:08.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:08.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:08.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:08.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:08.546][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2022-10-18 23:50:08.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:08.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:08.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:08.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:08.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:08.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:08.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:08.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:08.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:08.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:08.611][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.DEBUG[2022-10-18 23:50:08.613][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2022-10-18 23:50:08.615][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:08.618][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2022-10-18 23:50:08.620][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:08.622][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:08.624][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:08.626][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:08.629][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:08.631][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:08.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:08.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:08.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:08.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:08.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:08.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:08.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:08.659][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2022-10-18 23:50:08.665][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:08.667][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:08.669][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2022-10-18 23:50:09.119][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2022-10-18 23:50:09.604][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:09.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2022-10-18 23:50:09.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2022-10-18 23:50:09.667][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2022-10-18 23:50:09.676][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:09.705][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:09.708][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:09.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:09.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:09.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:09.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:09.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:09.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:09.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:09.732][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:09.734][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:09.736][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.738][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:09.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:09.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.753][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:09.755][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:09.757][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.758][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.760][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:09.762][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:09.764][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.766][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.769][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:09.771][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:09.773][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.774][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.776][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:09.779][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:09.781][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.783][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.785][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:09.787][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:09.789][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.791][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.793][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:09.796][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.797][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.798][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.800][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:09.802][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:09.804][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.806][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.808][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:09.811][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:09.813][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.815][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:09.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:09.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.833][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:09.836][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:09.838][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.840][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.842][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:09.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:09.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.854][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:09.856][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:09.857][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.858][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:09.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:09.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:09.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:09.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:09.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:09.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:09.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:09.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:09.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:09.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:09.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:09.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:09.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:09.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:09.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:09.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:09.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:09.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:09.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:09.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:09.935][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2022-10-18 23:50:09.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:09.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:09.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:09.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:09.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:09.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:09.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:09.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:09.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:09.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:09.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:09.991][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2022-10-18 23:50:09.992][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:09.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2022-10-18 23:50:09.997][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:09.999][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:10.001][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:10.003][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:10.006][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:10.007][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:10.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:10.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:10.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:10.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:10.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:10.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:10.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:10.031][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2022-10-18 23:50:10.036][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:10.038][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:10.041][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2022-10-18 23:50:10.485][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2022-10-18 23:50:10.952][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:10.968][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2022-10-18 23:50:10.992][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2022-10-18 23:50:11.012][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2022-10-18 23:50:11.021][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:11.078][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:11.081][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:11.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:11.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:11.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:11.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:11.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:11.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:11.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:11.112][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:11.114][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:11.116][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.118][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:11.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:11.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.134][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:11.137][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:11.139][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.141][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.143][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:11.145][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:11.147][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.150][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.153][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:11.155][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:11.158][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.160][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.162][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:11.164][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:11.166][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.168][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.171][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:11.173][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:11.175][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.177][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.180][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:11.182][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.185][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.187][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.190][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:11.193][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:11.195][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.198][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.201][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:11.204][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:11.206][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.208][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:11.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:11.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.229][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:11.232][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:11.234][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.236][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.239][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:11.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:11.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.256][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:11.258][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:11.260][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.262][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:11.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:11.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:11.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:11.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:11.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:11.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:11.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:11.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:11.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:11.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:11.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:11.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:11.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:11.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:11.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:11.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:11.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:11.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:11.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:11.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:11.360][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2022-10-18 23:50:11.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:11.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:11.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:11.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:11.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:11.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:11.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:11.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:11.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:11.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:11.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:11.431][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2022-10-18 23:50:11.433][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:11.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2022-10-18 23:50:11.440][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:11.443][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:11.445][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:11.448][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:11.450][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:11.453][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:11.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:11.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:11.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:11.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:11.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:11.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:11.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:11.482][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2022-10-18 23:50:11.489][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:11.491][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:11.494][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2022-10-18 23:50:11.987][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2022-10-18 23:50:12.497][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:12.514][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2022-10-18 23:50:12.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2022-10-18 23:50:12.565][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2022-10-18 23:50:12.574][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:12.608][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:12.610][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:12.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:12.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:12.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:12.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:12.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:12.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:12.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:12.638][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:12.641][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:12.643][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.645][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:12.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:12.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.662][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:12.664][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:12.666][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.668][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.671][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:12.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:12.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.686][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:12.689][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:12.691][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.693][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.696][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:12.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:12.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.725][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:12.728][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:12.730][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.732][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:12.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:12.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.748][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:12.750][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:12.752][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.754][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:12.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:12.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.771][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:12.774][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:12.776][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.778][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.780][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:12.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:12.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.795][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:12.797][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:12.799][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.800][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.803][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:12.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:12.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:12.821][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:12.823][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.825][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:12.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:12.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.843][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:12.845][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:12.848][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.850][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:12.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:12.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.870][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:12.873][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:12.875][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.877][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.879][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:12.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:12.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.894][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:12.896][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:12.898][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.901][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.903][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:12.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:12.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:12.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:12.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:12.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:12.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:12.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:12.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:12.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:12.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:12.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:12.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:12.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:12.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:12.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:12.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:12.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:12.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:12.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:12.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:12.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:12.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:13.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:13.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:13.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:13.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:13.009][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2022-10-18 23:50:13.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:13.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:13.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:13.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:13.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:13.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:13.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:13.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:13.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:13.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:13.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:13.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:13.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:13.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:13.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:13.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:13.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:13.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:13.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:13.059][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2022-10-18 23:50:13.061][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:13.065][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2022-10-18 23:50:13.067][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:13.070][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:13.073][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:13.075][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:13.077][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:13.079][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:13.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:13.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:13.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:13.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:13.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:13.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:13.104][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.DEBUG[2022-10-18 23:50:13.107][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2022-10-18 23:50:13.113][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:13.115][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:13.118][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2022-10-18 23:50:13.564][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2022-10-18 23:50:14.028][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:14.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2022-10-18 23:50:14.067][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2022-10-18 23:50:14.089][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2022-10-18 23:50:14.098][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:14.132][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:14.135][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:14.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:14.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:14.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:14.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:14.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:14.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:14.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:14.164][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:14.167][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:14.169][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.171][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:14.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:14.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.189][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:14.191][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:14.193][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.195][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.198][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:14.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:14.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.209][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:14.211][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:14.213][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.215][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.218][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:14.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:14.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.229][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:14.230][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:14.232][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.233][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:14.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:14.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.262][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:14.265][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:14.267][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.269][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:14.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:14.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.286][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:14.288][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:14.290][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.292][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.294][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:14.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:14.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.310][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:14.312][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:14.315][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.317][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.319][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:14.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:14.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.334][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:14.336][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:14.339][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.341][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:14.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:14.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.359][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:14.361][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:14.363][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.365][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:14.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:14.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.383][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:14.386][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:14.388][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.390][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.392][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:14.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:14.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.406][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:14.409][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:14.411][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.412][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.414][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:14.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:14.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:14.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:14.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:14.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:14.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:14.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:14.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:14.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:14.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:14.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:14.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:14.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:14.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:14.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:14.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:14.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:14.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:14.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:14.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:14.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:14.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:14.510][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2022-10-18 23:50:14.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:14.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:14.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:14.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:14.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:14.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:14.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:14.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:14.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:14.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:14.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:14.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:14.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:14.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:14.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:14.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:14.555][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2022-10-18 23:50:14.557][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:14.560][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2022-10-18 23:50:14.562][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:14.563][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:14.566][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:14.568][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:14.570][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:14.572][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:14.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:14.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:14.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:14.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:14.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:14.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:14.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:14.595][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2022-10-18 23:50:14.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:14.601][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:14.604][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2022-10-18 23:50:15.047][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2022-10-18 23:50:15.520][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:15.535][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2022-10-18 23:50:15.559][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2022-10-18 23:50:15.582][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2022-10-18 23:50:15.590][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:15.622][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:15.624][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:15.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:15.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:15.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:15.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:15.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:15.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:15.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:15.654][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:15.656][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:15.658][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.661][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:15.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:15.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.678][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:15.681][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:15.683][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.685][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.688][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:15.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:15.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.703][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:15.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:15.708][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.710][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:15.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:15.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.726][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:15.729][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:15.731][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.733][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:15.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:15.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.751][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:15.753][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:15.754][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.756][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:15.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:15.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.784][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:15.787][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:15.788][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.790][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.792][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:15.794][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:15.796][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.798][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.800][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:15.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:15.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.812][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:15.814][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:15.816][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.818][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:15.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:15.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.836][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:15.838][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:15.840][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.842][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:15.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:15.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.859][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:15.862][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:15.864][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.866][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.868][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:15.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:15.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.884][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:15.886][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:15.888][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.890][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:15.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:15.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:15.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:15.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:15.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:15.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:15.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:15.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:15.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:15.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:15.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:15.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:15.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:15.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:15.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:15.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:15.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:15.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:15.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:15.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:15.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:15.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:15.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:15.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:15.994][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2022-10-18 23:50:15.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:15.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:16.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:16.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:16.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:16.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:16.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:16.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:16.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:16.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:16.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:16.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:16.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:16.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:16.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:16.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:16.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:16.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:16.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:16.043][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2022-10-18 23:50:16.045][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:16.048][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2022-10-18 23:50:16.051][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:16.053][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:16.056][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:16.058][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:16.061][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:16.063][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:16.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:16.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:16.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:16.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:16.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:16.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:16.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:16.086][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2022-10-18 23:50:16.091][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:16.094][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:16.097][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2022-10-18 23:50:16.568][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2022-10-18 23:50:17.035][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:17.051][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2022-10-18 23:50:17.072][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2022-10-18 23:50:17.094][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2022-10-18 23:50:17.103][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:17.139][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:17.142][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:17.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:17.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:17.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:17.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:17.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:17.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:17.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:17.170][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:17.173][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:17.175][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.176][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:17.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:17.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.193][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:17.195][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:17.197][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.199][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.201][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:17.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:17.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.216][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:17.218][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:17.221][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.223][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:17.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:17.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.240][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:17.242][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:17.244][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.246][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:17.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:17.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.262][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:17.264][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:17.266][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.268][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:17.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:17.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.284][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:17.286][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:17.288][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.290][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.292][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:17.294][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.296][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.298][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.301][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:17.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.330][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.332][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.333][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.334][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:17.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.349][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:17.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:17.352][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.353][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:17.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:17.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.369][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:17.371][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:17.373][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.375][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.377][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:17.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:17.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.389][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:17.390][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:17.392][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.393][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.394][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:17.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:17.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:17.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:17.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:17.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:17.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:17.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:17.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:17.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:17.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:17.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:17.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:17.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:17.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:17.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:17.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:17.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:17.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:17.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:17.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:17.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:17.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:17.493][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2022-10-18 23:50:17.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:17.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:17.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:17.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:17.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:17.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:17.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:17.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:17.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:17.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:17.539][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[2022-10-18 23:50:17.542][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2022-10-18 23:50:17.544][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:17.547][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2022-10-18 23:50:17.549][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:17.551][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:17.553][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:17.555][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:17.558][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:17.560][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:17.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:17.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:17.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:17.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:17.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:17.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:17.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:17.589][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2022-10-18 23:50:17.595][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:17.596][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:17.599][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2022-10-18 23:50:18.136][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2022-10-18 23:50:18.612][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:18.627][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2022-10-18 23:50:18.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2022-10-18 23:50:18.668][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2022-10-18 23:50:18.675][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:18.704][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:18.705][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:18.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:18.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:18.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:18.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:18.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:18.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:18.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:18.727][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:18.729][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:18.730][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.731][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:18.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:18.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.745][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:18.747][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:18.749][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.751][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.754][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:18.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:18.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.768][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:18.770][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:18.771][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.773][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:18.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:18.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.787][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:18.789][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:18.790][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.791][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:18.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:18.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.807][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:18.809][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:18.811][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.813][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:18.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:18.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.827][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:18.829][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:18.831][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.833][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.835][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:18.837][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:18.838][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.840][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.842][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:18.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:18.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.855][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:18.858][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:18.859][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.861][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:18.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:18.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.874][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:18.875][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:18.877][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.878][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:18.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:18.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.905][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:18.907][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:18.909][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.911][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.913][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:18.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:18.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.926][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:18.928][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:18.930][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.932][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.935][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:18.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:18.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:18.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:18.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:18.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:18.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:18.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:18.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:18.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:18.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:18.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:18.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:18.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:18.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:18.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:18.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:18.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:18.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:19.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:19.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:19.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:19.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:19.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:19.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:19.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:19.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:19.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:19.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:19.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:19.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:19.024][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2022-10-18 23:50:19.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:19.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:19.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:19.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:19.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:19.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:19.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:19.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:19.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:19.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:19.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:19.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:19.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:19.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:19.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:19.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:19.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:19.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:19.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:19.066][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2022-10-18 23:50:19.068][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:19.070][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2022-10-18 23:50:19.072][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:19.073][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:19.075][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:19.076][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:19.078][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:19.079][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:19.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:19.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:19.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:19.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:19.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:19.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:19.104][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.DEBUG[2022-10-18 23:50:19.106][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2022-10-18 23:50:19.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:19.112][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:19.115][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2022-10-18 23:50:19.569][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2022-10-18 23:50:20.031][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:20.048][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2022-10-18 23:50:20.072][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2022-10-18 23:50:20.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2022-10-18 23:50:20.106][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:20.138][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:20.141][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:20.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:20.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:20.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:20.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:20.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:20.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:20.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:20.169][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:20.171][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:20.173][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.175][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:20.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:20.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.192][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:20.194][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:20.196][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.199][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.201][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:20.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:20.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.216][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:20.218][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:20.220][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.221][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.224][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:20.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:20.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.240][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:20.242][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:20.244][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.247][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:20.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:20.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.264][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:20.266][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:20.269][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.271][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:20.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:20.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.289][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:20.291][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:20.294][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.296][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.298][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:20.300][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:20.302][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.304][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.307][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:20.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:20.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.317][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:20.320][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:20.322][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.324][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:20.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:20.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.342][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:20.345][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:20.347][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.349][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:20.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:20.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.366][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:20.368][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:20.370][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.372][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.374][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:20.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:20.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.403][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:20.405][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:20.406][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.407][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.409][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:20.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:20.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:20.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:20.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:20.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:20.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:20.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:20.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:20.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:20.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:20.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:20.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:20.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:20.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:20.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:20.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:20.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:20.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:20.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:20.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:20.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:20.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:20.506][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2022-10-18 23:50:20.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:20.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:20.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:20.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:20.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:20.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:20.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:20.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:20.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:20.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:20.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:20.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:20.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:20.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:20.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:20.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:20.550][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2022-10-18 23:50:20.552][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:20.555][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2022-10-18 23:50:20.557][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:20.559][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:20.562][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:20.564][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:20.567][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:20.569][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:20.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:20.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:20.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:20.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:20.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:20.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:20.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:20.598][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2022-10-18 23:50:20.604][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:20.606][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:20.609][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2022-10-18 23:50:21.090][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2022-10-18 23:50:21.573][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:21.589][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2022-10-18 23:50:21.611][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2022-10-18 23:50:21.631][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2022-10-18 23:50:21.639][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:21.671][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:21.674][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:21.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:21.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:21.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:21.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:21.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:21.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:21.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:21.704][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:21.706][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:21.708][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.710][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:21.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:21.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.728][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:21.730][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:21.732][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.734][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.736][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:21.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:21.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.750][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:21.752][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:21.754][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.756][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:21.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:21.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.774][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:21.776][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:21.779][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.781][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:21.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:21.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.799][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:21.801][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:21.804][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.806][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:21.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:21.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.823][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:21.826][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:21.828][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.830][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.833][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:21.836][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:21.838][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.840][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.843][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:21.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:21.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.859][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:21.861][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:21.864][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.866][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:21.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:21.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.883][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:21.886][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:21.889][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.891][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:21.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:21.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.910][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:21.912][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:21.914][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.916][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.919][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:21.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:21.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.934][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:21.936][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:21.939][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.941][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.944][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:21.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:21.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:21.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:21.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:21.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:21.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:21.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:21.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:21.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:21.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:22.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:22.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:22.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:22.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:22.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:22.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:22.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:22.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:22.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:22.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:22.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:22.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:22.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:22.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:22.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:22.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:22.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:22.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:22.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:22.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:22.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:22.070][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2022-10-18 23:50:22.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:22.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:22.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:22.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:22.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:22.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:22.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:22.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:22.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:22.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:22.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:22.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:22.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:22.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:22.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:22.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:22.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:22.122][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2022-10-18 23:50:22.124][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:22.128][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2022-10-18 23:50:22.131][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:22.133][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:22.135][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:22.138][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:22.140][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:22.141][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:22.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:22.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:22.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:22.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:22.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:22.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:22.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:22.170][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2022-10-18 23:50:22.176][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:22.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:22.181][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2022-10-18 23:50:22.649][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2022-10-18 23:50:23.125][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:23.142][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2022-10-18 23:50:23.165][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2022-10-18 23:50:23.185][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2022-10-18 23:50:23.195][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:23.230][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:23.232][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:23.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:23.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:23.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:23.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:23.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:23.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:23.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:23.260][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:23.262][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:23.263][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.265][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:23.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:23.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.278][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:23.280][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:23.281][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.282][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.284][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:23.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:23.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.295][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:23.298][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:23.300][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.302][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.304][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:23.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:23.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.318][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:23.320][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:23.322][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.324][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:23.329][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:23.331][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.333][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:23.337][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:23.339][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.341][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.344][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:23.346][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:23.348][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.349][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.352][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:23.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:23.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.366][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:23.369][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:23.371][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.373][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:23.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:23.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.389][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:23.391][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:23.393][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.395][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:23.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:23.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.409][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:23.411][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:23.412][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.413][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.415][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:23.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:23.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.428][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:23.430][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:23.432][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.434][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:23.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:23.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:23.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:23.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:23.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:23.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:23.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:23.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:23.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:23.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:23.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:23.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:23.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:23.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:23.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:23.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:23.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:23.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:23.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:23.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:23.535][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2022-10-18 23:50:23.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:23.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:23.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:23.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:23.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:23.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:23.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:23.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:23.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:23.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:23.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:23.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:23.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:23.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:23.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:23.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:23.575][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2022-10-18 23:50:23.576][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:23.579][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2022-10-18 23:50:23.582][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:23.584][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:23.585][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:23.587][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:23.589][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:23.590][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:23.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:23.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:23.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:23.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:23.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:23.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:23.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:23.617][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2022-10-18 23:50:23.623][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:23.624][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:23.626][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2022-10-18 23:50:24.085][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2022-10-18 23:50:24.594][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:24.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2022-10-18 23:50:24.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2022-10-18 23:50:24.659][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2022-10-18 23:50:24.668][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:24.703][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:24.704][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:24.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:24.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:24.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:24.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:24.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:24.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:24.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:24.731][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:24.734][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:24.736][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.738][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:24.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:24.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.756][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:24.759][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:24.761][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.763][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.766][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:24.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:24.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.779][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:24.782][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:24.784][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.786][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:24.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:24.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.802][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:24.804][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:24.806][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.808][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.810][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:24.813][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:24.815][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.817][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.819][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:24.821][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:24.823][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.825][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.827][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:24.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:24.831][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.833][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.835][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:24.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:24.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.847][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:24.849][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:24.851][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.853][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:24.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:24.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.870][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:24.872][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:24.874][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.876][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:24.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:24.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.895][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:24.897][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:24.899][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.901][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.903][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:24.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:24.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.916][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:24.917][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:24.919][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.921][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:24.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:24.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:24.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:24.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:24.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:24.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:24.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:24.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:24.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:24.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:24.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:24.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:24.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:24.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:24.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:24.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:24.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:24.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:24.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:24.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:25.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:25.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:25.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:25.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:25.009][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2022-10-18 23:50:25.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:25.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:25.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:25.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:25.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:25.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:25.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:25.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:25.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:25.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:25.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:25.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:25.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:25.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:25.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:25.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:25.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:25.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:25.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:25.054][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2022-10-18 23:50:25.056][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:25.060][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2022-10-18 23:50:25.063][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:25.065][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:25.067][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:25.084][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:25.086][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:25.087][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:25.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:25.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:25.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:25.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:25.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:25.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:25.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:25.115][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2022-10-18 23:50:25.121][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:25.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:25.126][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2022-10-18 23:50:25.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2022-10-18 23:50:26.154][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:26.170][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2022-10-18 23:50:26.194][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2022-10-18 23:50:26.213][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2022-10-18 23:50:26.221][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:26.254][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:26.256][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:26.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:26.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:26.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:26.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:26.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:26.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:26.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:26.283][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:26.286][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:26.287][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.289][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:26.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:26.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.303][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:26.305][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:26.307][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.309][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.311][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:26.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:26.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.325][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:26.327][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:26.329][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.330][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:26.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:26.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.345][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:26.347][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:26.349][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.351][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:26.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:26.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.368][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:26.370][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:26.372][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.374][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:26.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:26.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.390][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:26.393][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:26.394][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.395][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.398][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:26.400][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:26.402][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.404][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.406][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:26.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:26.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.421][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:26.423][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:26.426][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.428][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:26.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:26.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.443][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:26.445][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:26.447][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.449][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.452][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:26.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:26.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.466][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:26.468][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:26.470][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.472][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.475][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:26.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:26.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.488][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:26.491][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:26.492][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.494][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.497][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:26.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:26.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:26.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:26.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:26.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:26.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:26.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:26.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:26.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:26.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:26.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:26.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:26.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:26.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:26.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:26.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:26.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:26.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:26.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:26.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:26.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:26.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:26.598][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2022-10-18 23:50:26.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:26.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:26.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:26.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:26.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:26.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:26.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:26.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:26.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:26.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:26.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:26.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:26.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:26.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:26.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:26.643][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[2022-10-18 23:50:26.646][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2022-10-18 23:50:26.648][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:26.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2022-10-18 23:50:26.655][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:26.657][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:26.660][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:26.662][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:26.664][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:26.666][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:26.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:26.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:26.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:26.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:26.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:26.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:26.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:26.707][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2022-10-18 23:50:26.712][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:26.714][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:26.716][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2022-10-18 23:50:27.159][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2022-10-18 23:50:27.615][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:27.628][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2022-10-18 23:50:27.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2022-10-18 23:50:27.673][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2022-10-18 23:50:27.682][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:27.714][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:27.717][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:27.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:27.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:27.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:27.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:27.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:27.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:27.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:27.745][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:27.747][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:27.749][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.750][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:27.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:27.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.761][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:27.763][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:27.764][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.765][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.767][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:27.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:27.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.782][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:27.785][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:27.787][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.789][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.791][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:27.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:27.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.806][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:27.808][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:27.810][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.812][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:27.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:27.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.830][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:27.832][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:27.834][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.836][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:27.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:27.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.851][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:27.854][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:27.856][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.858][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.860][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:27.862][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:27.863][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.865][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.867][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:27.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:27.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.881][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:27.883][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:27.885][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.887][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:27.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:27.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.902][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:27.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:27.906][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.909][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:27.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:27.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.924][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:27.926][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:27.927][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.928][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.930][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:27.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:27.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:27.945][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:27.947][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.949][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.951][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:27.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:27.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:27.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:27.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:27.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:27.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:27.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:27.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:27.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:27.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:27.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:27.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:28.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:28.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:28.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:28.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:28.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:28.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:28.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:28.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:28.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:28.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:28.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:28.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:28.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:28.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:28.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:28.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:28.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:28.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:28.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:28.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:28.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:28.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:28.063][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2022-10-18 23:50:28.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:28.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:28.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:28.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:28.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:28.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:28.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:28.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:28.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:28.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:28.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:28.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:28.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:28.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:28.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:28.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:28.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:28.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:28.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:28.110][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2022-10-18 23:50:28.111][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:28.115][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2022-10-18 23:50:28.117][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:28.120][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:28.122][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:28.125][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:28.127][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:28.129][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:28.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:28.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:28.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:28.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:28.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:28.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:28.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:28.156][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2022-10-18 23:50:28.160][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:28.162][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:28.164][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2022-10-18 23:50:29.707][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2022-10-18 23:50:30.187][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:30.203][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2022-10-18 23:50:30.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2022-10-18 23:50:30.250][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2022-10-18 23:50:30.259][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:30.291][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:30.293][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:30.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:30.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:30.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:30.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:30.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:30.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:30.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:30.321][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:30.323][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:30.325][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.327][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:30.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:30.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.344][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:30.345][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:30.347][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.349][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.352][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:30.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:30.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.366][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:30.368][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:30.370][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.371][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.374][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:30.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:30.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.386][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:30.389][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:30.390][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.393][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:30.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:30.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.409][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:30.411][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:30.413][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.414][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:30.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:30.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.430][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:30.433][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:30.435][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.437][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.440][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:30.442][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:30.444][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.446][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.449][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:30.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:30.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.463][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:30.465][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:30.467][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.469][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:30.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:30.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.485][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:30.488][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:30.490][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.493][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:30.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:30.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.511][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:30.514][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:30.516][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.518][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.520][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:30.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:30.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.535][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:30.537][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:30.539][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.541][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.544][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:30.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:30.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:30.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:30.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:30.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:30.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:30.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:30.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:30.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:30.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:30.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:30.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:30.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:30.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:30.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:30.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:30.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:30.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:30.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:30.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:30.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:30.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:30.642][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2022-10-18 23:50:30.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:30.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:30.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:30.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:30.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:30.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:30.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:30.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:30.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:30.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:30.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:30.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:30.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:30.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:30.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:30.687][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[2022-10-18 23:50:30.690][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2022-10-18 23:50:30.692][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:30.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2022-10-18 23:50:30.697][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:30.700][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:30.702][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:30.704][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:30.706][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:30.708][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:30.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:30.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:30.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:30.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:30.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:30.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:30.732][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[2022-10-18 23:50:30.734][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2022-10-18 23:50:30.740][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:30.742][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:30.744][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2022-10-18 23:50:31.187][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2022-10-18 23:50:31.671][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:31.687][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2022-10-18 23:50:31.711][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2022-10-18 23:50:31.734][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2022-10-18 23:50:31.743][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:31.777][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:31.779][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:31.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:31.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:31.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:31.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:31.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:31.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:31.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:31.807][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:31.810][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:31.812][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.813][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:31.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:31.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.830][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:31.832][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:31.834][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.836][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.838][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:31.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:31.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.852][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:31.854][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:31.856][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.858][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.861][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:31.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:31.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.875][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:31.877][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:31.879][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.881][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:31.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:31.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.898][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:31.901][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:31.903][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.904][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:31.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:31.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.920][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:31.923][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:31.925][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.927][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.930][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:31.932][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:31.934][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.936][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.939][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:31.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:31.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.953][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:31.955][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:31.958][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.959][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:31.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:31.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.976][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:31.978][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:31.980][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.982][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:31.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:31.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:31.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:31.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.001][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:32.003][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:32.006][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.008][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.011][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:32.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:32.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.026][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:32.028][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:32.031][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.033][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:32.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:32.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:32.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:32.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:32.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:32.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:32.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:32.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:32.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:32.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:32.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:32.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:32.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:32.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:32.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:32.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:32.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:32.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:32.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:32.140][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2022-10-18 23:50:32.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:32.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:32.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:32.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:32.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:32.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:32.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:32.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:32.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:32.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:32.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:32.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:32.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:32.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:32.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:32.191][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[2022-10-18 23:50:32.194][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2022-10-18 23:50:32.196][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:32.200][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2022-10-18 23:50:32.203][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:32.205][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:32.207][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:32.209][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:32.211][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:32.213][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:32.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:32.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:32.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:32.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:32.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:32.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:32.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:32.242][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2022-10-18 23:50:32.248][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:32.249][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:32.252][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2022-10-18 23:50:32.723][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2022-10-18 23:50:33.206][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:33.222][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2022-10-18 23:50:33.247][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2022-10-18 23:50:33.270][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2022-10-18 23:50:33.278][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:33.309][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:33.311][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:33.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:33.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:33.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:33.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:33.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:33.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:33.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:33.339][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:33.341][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:33.344][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.346][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:33.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:33.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.362][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:33.365][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:33.367][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.369][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.371][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:33.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:33.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.387][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:33.389][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:33.392][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.394][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.397][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:33.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:33.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.412][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:33.415][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:33.418][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.421][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:33.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:33.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.441][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:33.443][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:33.445][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.447][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:33.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:33.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.464][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:33.466][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:33.468][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.469][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.472][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:33.474][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.476][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.477][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.480][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:33.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.493][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.495][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.497][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.500][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:33.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.523][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:33.526][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:33.528][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.530][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:33.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:33.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.547][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:33.549][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:33.550][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.552][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.555][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:33.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:33.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.566][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:33.567][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:33.568][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.570][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.573][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:33.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:33.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:33.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:33.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:33.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:33.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:33.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:33.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:33.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:33.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:33.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:33.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:33.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:33.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:33.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:33.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:33.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:33.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:33.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:33.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:33.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:33.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:33.677][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2022-10-18 23:50:33.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:33.773][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[2022-10-18 23:50:33.780][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:33.783][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 23:50:33.786][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:33.788][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-10-18 23:50:33.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:33.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:33.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:33.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:33.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:33.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:33.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:33.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:33.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:33.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:33.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:33.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:33.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:33.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:33.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:33.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:33.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:33.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:33.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:33.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:33.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:33.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:33.968][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.TRACE[2022-10-18 23:50:33.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:33.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:33.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:33.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.137][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[2022-10-18 23:50:34.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.562][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.621][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.TRACE[2022-10-18 23:50:34.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:34.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:34.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:34.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:34.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:34.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:34.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:34.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:34.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:34.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:34.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:34.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:34.863][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[2022-10-18 23:50:34.870][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:34.872][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:34.877][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:35.337][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:35.804][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:35.820][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2022-10-18 23:50:35.847][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2022-10-18 23:50:35.859][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:35.867][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:35.869][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:35.874][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:36.320][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:36.788][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:36.803][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2022-10-18 23:50:36.851][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2022-10-18 23:50:36.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:36.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:36.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:36.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:36.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:36.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:36.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:36.895][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2022-10-18 23:50:36.897][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:36.901][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2022-10-18 23:50:36.903][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:36.905][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:36.908][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:36.910][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:36.912][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:36.914][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:36.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:36.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:36.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:36.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:36.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:36.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:36.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:36.942][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2022-10-18 23:50:36.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:36.951][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:36.954][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2022-10-18 23:50:37.411][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2022-10-18 23:50:37.882][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:37.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2022-10-18 23:50:37.922][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2022-10-18 23:50:37.948][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2022-10-18 23:50:37.958][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:37.991][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:37.993][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:37.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:37.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:38.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:38.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:38.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:38.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:38.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:38.021][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:38.022][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:38.024][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.026][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:38.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:38.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.043][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:38.045][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:38.047][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.049][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.052][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:38.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:38.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.066][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:38.069][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:38.071][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.072][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.075][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:38.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:38.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.088][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:38.090][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:38.093][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.095][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:38.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:38.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.113][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:38.116][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:38.118][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.120][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:38.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:38.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.138][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:38.140][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:38.142][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.144][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.147][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:38.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:38.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.161][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:38.164][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:38.166][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.168][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.170][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:38.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:38.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.186][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.188][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.190][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.192][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.210][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:38.212][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:38.215][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.217][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:38.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:38.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.235][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:38.238][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:38.240][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.242][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.244][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:38.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:38.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.258][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:38.262][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:38.264][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.267][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.269][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:38.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:38.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:38.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:38.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:38.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:38.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:38.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:38.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:38.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:38.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:38.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:38.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:38.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:38.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:38.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:38.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:38.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:38.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:38.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:38.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:38.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:38.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:38.372][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2022-10-18 23:50:38.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:38.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:38.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:38.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:38.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:38.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:38.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:38.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:38.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:38.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:38.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:38.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:38.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:38.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:38.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:38.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:38.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:38.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:38.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:38.485][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2022-10-18 23:50:38.487][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:38.491][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2022-10-18 23:50:38.493][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:38.496][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:38.498][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:38.501][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:38.503][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:38.505][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:38.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:38.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:38.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:38.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:38.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:38.529][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:38.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:38.533][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2022-10-18 23:50:38.538][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:38.540][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:38.543][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2022-10-18 23:50:38.983][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2022-10-18 23:50:39.457][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:39.472][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2022-10-18 23:50:39.494][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2022-10-18 23:50:39.516][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2022-10-18 23:50:39.524][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:39.562][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:39.564][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:39.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:39.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:39.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:39.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:39.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:39.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:39.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:39.590][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:39.592][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:39.594][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.596][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:39.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:39.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.613][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:39.616][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:39.618][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.619][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.621][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:39.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:39.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.635][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:39.637][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:39.639][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.641][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.644][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:39.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:39.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.659][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:39.661][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:39.663][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.665][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:39.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:39.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.682][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:39.684][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:39.686][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.688][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:39.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:39.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.706][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:39.709][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:39.711][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.713][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.715][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:39.716][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:39.718][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.720][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.722][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:39.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:39.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.736][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.739][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.741][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.743][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.758][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:39.761][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:39.763][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.765][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:39.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:39.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.782][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:39.785][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:39.787][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.789][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.791][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:39.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:39.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.805][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:39.807][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:39.809][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.811][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.814][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:39.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:39.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:39.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:39.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:39.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:39.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:39.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:39.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:39.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:39.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:39.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:39.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:39.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:39.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:39.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:39.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:39.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:39.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:39.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:39.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:39.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:39.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:39.918][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2022-10-18 23:50:39.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:39.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:39.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:39.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.046][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[2022-10-18 23:50:40.053][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:40.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 23:50:40.059][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:40.062][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-10-18 23:50:40.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.230][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.TRACE[2022-10-18 23:50:40.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.298][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[2022-10-18 23:50:40.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.683][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.TRACE[2022-10-18 23:50:40.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.773][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.TRACE[2022-10-18 23:50:40.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.811][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[2022-10-18 23:50:40.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:40.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:40.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:40.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:40.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:40.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:40.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:40.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:40.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:40.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:40.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:40.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.085][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[2022-10-18 23:50:41.092][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:41.095][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 23:50:41.097][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:41.100][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-10-18 23:50:41.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:41.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.205][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.TRACE[2022-10-18 23:50:41.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:41.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.406][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.TRACE[2022-10-18 23:50:41.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:41.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:41.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.539][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.TRACE[2022-10-18 23:50:41.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.587][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[2022-10-18 23:50:41.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.633][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[2022-10-18 23:50:41.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:41.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.719][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[2022-10-18 23:50:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:41.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:41.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:41.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.900][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.TRACE[2022-10-18 23:50:41.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.943][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.TRACE[2022-10-18 23:50:41.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:41.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:41.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:41.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:41.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:41.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:41.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:41.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:41.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:41.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:41.996][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.TRACE[2022-10-18 23:50:41.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.057][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:42.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:42.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:42.087][biodb::testThat]
biodb.INFO [2022-10-18 23:50:42.089][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-10-18 23:50:42.091][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:42.093][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:42.099][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 23:50:42.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 23:50:42.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:42.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:42.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:42.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:42.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:42.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:42.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:42.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:42.258][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[2022-10-18 23:50:42.265][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:42.268][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2022-10-18 23:50:42.270][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:42.273][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2022-10-18 23:50:42.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:42.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:42.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:42.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:42.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:42.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:42.300][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[2022-10-18 23:50:42.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:42.327][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[2022-10-18 23:50:42.334][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:42.337][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2022-10-18 23:50:42.339][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:42.341][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2022-10-18 23:50:42.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:42.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:42.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:42.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:42.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:42.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:42.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:42.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:42.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:42.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:42.401][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:42.404][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2022-10-18 23:50:42.406][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:42.409][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2022-10-18 23:50:42.414][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:50:42.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:42.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:42.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:42.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:42.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:42.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:42.436][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[2022-10-18 23:50:42.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.453][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:42.455][private$selectFields]
biodb.TRACE[2022-10-18 23:50:42.457][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:42.459][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:42.461][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:42.463][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.465][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.468][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.470][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.472][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.476][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.478][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.481][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:42.483][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:42.485][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.487][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.489][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.491][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.493][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:42.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.535][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2022-10-18 23:50:42.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:42.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:42.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:42.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:42.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:42.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:42.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:42.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.573][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:42.575][private$selectFields]
biodb.TRACE[2022-10-18 23:50:42.577][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:42.579][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:42.581][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:42.583][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.585][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.587][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.588][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.590][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.592][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.593][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.595][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.597][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:42.598][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:42.600][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.602][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.604][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.606][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.607][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:42.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:42.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.641][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 23:50:42.643][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:50:42.644][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 23:50:42.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:42.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:42.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:42.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:42.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:42.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:42.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:42.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:42.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:42.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:42.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:42.936][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:42.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:42.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:42.951][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:43.396][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:43.862][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2022-10-18 23:50:43.869][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2022-10-18 23:50:43.878][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2022-10-18 23:50:43.920][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2022-10-18 23:50:43.933][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:43.940][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:43.941][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:43.945][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:44.384][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:44.847][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:44.862][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2022-10-18 23:50:44.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2022-10-18 23:50:44.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:44.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:44.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:44.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:44.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:44.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:44.918][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[2022-10-18 23:50:44.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:44.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:44.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:44.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:44.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:44.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:44.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:44.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:44.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:44.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:44.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:44.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:44.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:44.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:44.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:44.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:44.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:44.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:44.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:44.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:44.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:44.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:44.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:44.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:45.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:45.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:45.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:45.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:45.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:45.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:45.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:45.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:45.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:45.117][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:50:45.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:45.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:45.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:45.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:45.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:45.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:45.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:45.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.213][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.214][private$selectFields]
biodb.TRACE[2022-10-18 23:50:45.216][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:45.217][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:45.218][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.219][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.222][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.223][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.224][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.228][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.230][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.232][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.235][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.237][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.239][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.241][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.244][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.246][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:45.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.276][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-10-18 23:50:45.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:45.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:45.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:45.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:45.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:45.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:45.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:45.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.397][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.399][private$selectFields]
biodb.TRACE[2022-10-18 23:50:45.401][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:45.403][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:45.405][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.408][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.411][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.413][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.415][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.418][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.420][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.422][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.423][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.448][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.450][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.452][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.454][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.456][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.458][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:45.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.485][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 23:50:45.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:45.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:45.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:45.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:45.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:45.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:45.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:45.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.529][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.531][private$selectFields]
biodb.TRACE[2022-10-18 23:50:45.533][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:45.535][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:45.537][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.539][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.541][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.544][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.546][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.548][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.550][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.552][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.554][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.556][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.558][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:45.560][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.562][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.564][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.566][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.569][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:45.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:45.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.595][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-10-18 23:50:45.597][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:50:45.599][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 23:50:45.625][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:45.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:45.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:45.635][biodb::testThat]
biodb.INFO [2022-10-18 23:50:45.637][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-10-18 23:50:45.639][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:45.642][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:45.648][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 23:50:45.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 23:50:45.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:45.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:45.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:45.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:45.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:45.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:45.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:45.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:45.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:45.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:45.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:45.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:45.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:45.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:45.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:45.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:45.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:45.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:45.816][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[2022-10-18 23:50:45.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:45.826][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:45.831][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:46.289][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:46.774][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:46.789][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2022-10-18 23:50:46.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2022-10-18 23:50:46.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:46.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:46.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:46.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:46.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:46.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:46.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:46.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:46.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:46.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:46.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:46.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:46.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:46.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:46.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:46.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:46.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:46.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:46.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:46.871][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:46.878][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:46.880][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:46.884][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:47.339][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:47.796][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:47.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2022-10-18 23:50:47.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2022-10-18 23:50:47.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:47.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:47.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:47.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:47.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:47.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:47.868][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[2022-10-18 23:50:47.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:47.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:47.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:47.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:47.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:47.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:47.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:47.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:47.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:47.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:47.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:47.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:47.897][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:47.904][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:47.906][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:47.910][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:48.368][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:48.869][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:48.885][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2022-10-18 23:50:48.911][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2022-10-18 23:50:48.922][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:50:48.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:48.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:48.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:48.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:48.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:48.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:48.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:48.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:48.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:48.964][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:48.966][private$selectFields]
biodb.TRACE[2022-10-18 23:50:48.968][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:48.970][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:48.972][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:48.974][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.977][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.978][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.980][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:48.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.985][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.987][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.988][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:48.990][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:48.992][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:48.994][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.996][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:48.997][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:48.999][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.001][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:49.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.028][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2022-10-18 23:50:49.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:49.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.069][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.071][private$selectFields]
biodb.TRACE[2022-10-18 23:50:49.074][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:49.076][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:49.078][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.080][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.082][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.084][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.086][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.088][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.091][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.093][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.095][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.097][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.099][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.101][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.103][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.105][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.107][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.109][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:49.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.137][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 23:50:49.140][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:50:49.142][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 23:50:49.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:49.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.227][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[2022-10-18 23:50:49.319][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[2022-10-18 23:50:49.326][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:49.329][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2022-10-18 23:50:49.332][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:49.335][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2022-10-18 23:50:49.341][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[2022-10-18 23:50:49.346][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:49.348][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2022-10-18 23:50:49.350][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:49.352][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2022-10-18 23:50:49.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:49.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:49.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:49.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:49.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.472][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.TRACE[2022-10-18 23:50:49.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:49.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:49.499][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:50:49.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.523][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[2022-10-18 23:50:49.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.551][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.553][private$selectFields]
biodb.TRACE[2022-10-18 23:50:49.555][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:49.557][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:49.558][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.560][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.562][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.564][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.565][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.567][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.569][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.571][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.573][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.575][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.578][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.579][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.582][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.584][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.586][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.588][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:49.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.617][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-10-18 23:50:49.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:49.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.658][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.660][private$selectFields]
biodb.TRACE[2022-10-18 23:50:49.663][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:49.665][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:49.667][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.669][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.673][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.675][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.677][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.680][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.682][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.684][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.686][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.688][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.690][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.692][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.694][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.696][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.698][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:49.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.725][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 23:50:49.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:49.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.769][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.771][private$selectFields]
biodb.TRACE[2022-10-18 23:50:49.773][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:49.775][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:49.777][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.779][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.781][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.783][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.785][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.787][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.790][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.792][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.794][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.796][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.798][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:49.800][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.802][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.804][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.806][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.808][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:49.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:49.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.836][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-10-18 23:50:49.838][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:50:49.839][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 23:50:49.856][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:49.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:49.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:49.867][biodb::testThat]
biodb.INFO [2022-10-18 23:50:49.869][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-10-18 23:50:49.871][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:49.873][biodb::testThat]
biodb.TRACE[2022-10-18 23:50:49.880][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 23:50:49.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 23:50:49.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:49.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:49.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:49.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:49.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:49.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:49.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:49.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:49.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:49.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:49.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:49.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:49.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:49.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:49.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:49.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:49.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:49.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:50.056][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[2022-10-18 23:50:50.064][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:50.067][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2022-10-18 23:50:50.070][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:50.073][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2022-10-18 23:50:50.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:50.130][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[2022-10-18 23:50:50.137][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:50.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2022-10-18 23:50:50.142][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:50.145][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2022-10-18 23:50:50.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:50.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:50.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:50.197][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:50.204][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:50.207][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2022-10-18 23:50:50.211][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:50.213][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2022-10-18 23:50:50.219][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:50:50.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.243][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[2022-10-18 23:50:50.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.274][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.277][private$selectFields]
biodb.TRACE[2022-10-18 23:50:50.279][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:50.281][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:50.283][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.285][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.288][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.290][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.292][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.294][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.297][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.299][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.301][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.303][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.305][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.307][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.309][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.311][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.313][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.316][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:50.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.345][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2022-10-18 23:50:50.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:50.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.385][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.387][private$selectFields]
biodb.TRACE[2022-10-18 23:50:50.389][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:50.391][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:50.394][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.396][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.398][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.401][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.403][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.406][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.409][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.411][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.413][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.418][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.420][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.422][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.424][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.426][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.428][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:50.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.457][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 23:50:50.459][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:50:50.461][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 23:50:50.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:50.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:50.673][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:50.681][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:50.684][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2022-10-18 23:50:50.687][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:50.690][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2022-10-18 23:50:50.696][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:50.703][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:50:50.706][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2022-10-18 23:50:50.709][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:50:50.712][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2022-10-18 23:50:50.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:50.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:50.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:50.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:50.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:50.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:50.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:50.856][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 23:50:50.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:50.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.895][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.897][private$selectFields]
biodb.TRACE[2022-10-18 23:50:50.899][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:50.901][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:50.903][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.905][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.909][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.911][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.914][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.916][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.918][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.920][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.922][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.924][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:50.926][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.928][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.931][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.933][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.935][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:50.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.971][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-10-18 23:50:50.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:50.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:50.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:50.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:50.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:50.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:50.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:50.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:50.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:50.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:50.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.006][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:51.007][private$selectFields]
biodb.TRACE[2022-10-18 23:50:51.009][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:51.011][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:51.013][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:51.015][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.017][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.019][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.021][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.024][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.026][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.027][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.030][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.032][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:51.034][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:51.036][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.038][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.039][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.040][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.042][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:51.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 23:50:51.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:51.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:51.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:51.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:51.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:51.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:51.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:51.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.109][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:51.111][private$selectFields]
biodb.TRACE[2022-10-18 23:50:51.113][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 23:50:51.115][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 23:50:51.117][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:51.119][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.121][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.123][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.125][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.127][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.130][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.132][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.134][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.135][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:51.137][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 23:50:51.138][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.140][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.141][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.143][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.145][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 23:50:51.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:51.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:51.172][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-10-18 23:50:51.174][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 23:50:51.177][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 23:50:51.218][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:51.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 23:50:51.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:51.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:51.228][biodb::testThat]
biodb.INFO [2022-10-18 23:50:51.230][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2022-10-18 23:50:51.232][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:51.234][biodb::testThat]
biodb.DEBUG[2022-10-18 23:50:51.238][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-10-18 23:50:51.240][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:50:51.244][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-10-18 23:50:51.246][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:50:51.249][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:51.250][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:51.252][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:51.254][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:51.256][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:51.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:51.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:51.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:51.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:51.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:51.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:51.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:51.284][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2022-10-18 23:50:51.290][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:51.293][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:51.295][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2022-10-18 23:50:51.763][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2022-10-18 23:50:52.227][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:52.241][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2022-10-18 23:50:52.267][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2022-10-18 23:50:52.290][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2022-10-18 23:50:52.299][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:52.331][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:50:52.333][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:52.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:52.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:52.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:52.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:52.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:52.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:52.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:52.360][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:52.362][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:52.364][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.365][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:52.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:52.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.382][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:52.384][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:52.387][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.389][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.391][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:52.394][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:52.396][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.398][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.401][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:52.403][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:52.405][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.408][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.411][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:52.414][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:52.417][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.419][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.421][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:52.423][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:52.425][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.427][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.429][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:52.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:52.433][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.435][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.437][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:52.439][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:52.441][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.443][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.445][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:52.447][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:52.449][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.451][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.454][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:52.456][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:52.457][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.458][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.460][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:52.478][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:52.480][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.482][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:52.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:52.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:52.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:52.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:52.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:52.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:52.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:52.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:52.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:52.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:52.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:52.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:52.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:52.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:52.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:52.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:52.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:52.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:52.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:52.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:52.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:52.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:52.562][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2022-10-18 23:50:52.564][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2022-10-18 23:50:52.574][biodb::testThat]
biodb.INFO [2022-10-18 23:50:52.577][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-10-18 23:50:52.578][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:52.580][biodb::testThat]
biodb.DEBUG[2022-10-18 23:50:52.600][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2022-10-18 23:50:52.602][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2022-10-18 23:50:52.604][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2022-10-18 23:50:52.607][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2022-10-18 23:50:52.610][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2022-10-18 23:50:52.612][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:50:52.615][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:50:52.617][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:52.619][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:50:52.621][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:50:52.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:52.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:52.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:52.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:52.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:52.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:52.647][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[2022-10-18 23:50:52.649][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2022-10-18 23:50:52.657][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:52.659][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:52.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2022-10-18 23:50:53.119][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2022-10-18 23:50:53.582][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:53.598][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2022-10-18 23:50:53.622][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2022-10-18 23:50:53.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:53.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:53.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:53.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:53.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:53.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:53.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:53.653][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2022-10-18 23:50:53.658][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:53.660][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:53.663][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2022-10-18 23:50:54.120][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2022-10-18 23:50:54.585][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:54.601][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2022-10-18 23:50:54.623][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2022-10-18 23:50:54.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:54.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:54.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:54.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:54.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:54.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:54.649][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.DEBUG[2022-10-18 23:50:54.652][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2022-10-18 23:50:54.658][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:54.660][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:54.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2022-10-18 23:50:55.113][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2022-10-18 23:50:55.577][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:55.592][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2022-10-18 23:50:55.616][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2022-10-18 23:50:55.666][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2022-10-18 23:50:55.674][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:50:55.702][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2022-10-18 23:50:55.705][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2022-10-18 23:50:55.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:55.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:55.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:55.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:55.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:55.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:55.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:55.730][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:55.732][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:55.734][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.736][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:55.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:55.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.751][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:55.753][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:55.755][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.757][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.759][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:55.761][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:55.763][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.765][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.767][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:55.769][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:55.771][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.773][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.776][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:55.778][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:55.780][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.782][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.784][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:55.786][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:55.788][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.790][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.793][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:55.795][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:55.797][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.800][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.802][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:55.804][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:55.806][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.808][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.811][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:55.813][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:55.815][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.817][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.820][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:55.822][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:55.824][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.826][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.829][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:55.831][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:55.833][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.835][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:55.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:55.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:55.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:55.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:55.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:55.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:55.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:55.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:55.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:55.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:55.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:55.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:55.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:55.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:55.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:55.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:55.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:55.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:55.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:55.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:55.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:55.930][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:55.932][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:55.934][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.937][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:55.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:55.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.954][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:55.956][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:55.958][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.960][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.962][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:55.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:55.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.976][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:55.979][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:55.980][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.982][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:55.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:55.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:55.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:55.999][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:56.001][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:56.003][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.004][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:56.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:56.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.021][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:56.024][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:56.026][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.028][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:56.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:56.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.044][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:56.046][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:56.048][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.051][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.053][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:56.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:56.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.067][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:56.070][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:56.072][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.074][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.076][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:56.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:56.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:56.094][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:56.096][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.097][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:56.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:56.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.114][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:56.116][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:56.118][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.120][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:56.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:56.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.137][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:56.139][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:56.141][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.142][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.145][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:56.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:56.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.160][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:56.162][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:56.165][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.167][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.170][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:56.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:56.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:56.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:50:56.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:56.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:56.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:56.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:56.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:56.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:50:56.275][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.277][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.279][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.281][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.298][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:56.300][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:56.302][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.304][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.307][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:50:56.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:50:56.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.321][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:56.323][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:56.324][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.326][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:50:56.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:50:56.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.352][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:56.355][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:56.357][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.358][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:50:56.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:50:56.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.374][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:56.376][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:56.377][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.379][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:50:56.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:50:56.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.396][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:56.399][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:56.401][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.403][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.406][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:56.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:50:56.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.420][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:56.423][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:56.425][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.427][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.430][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:50:56.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:50:56.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.444][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:56.446][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:56.448][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.450][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:56.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:56.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.467][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:56.469][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:56.471][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.473][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:56.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:56.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.489][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:56.490][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:56.492][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.494][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.496][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:50:56.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:50:56.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.508][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:56.511][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:56.513][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.515][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:50:56.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:50:56.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:50:56.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:56.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:50:56.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:50:56.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:56.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:50:56.674][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2022-10-18 23:50:56.676][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2022-10-18 23:50:56.678][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-10-18 23:50:56.701][biodb::testThat]
biodb.INFO [2022-10-18 23:50:56.703][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2022-10-18 23:50:56.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:56.707][biodb::testThat]
biodb.INFO [2022-10-18 23:50:56.753][biodb::testThat]
biodb.INFO [2022-10-18 23:50:56.755][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2022-10-18 23:50:56.757][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:56.759][biodb::testThat]
biodb.INFO [2022-10-18 23:50:56.771][biodb::testThat]
biodb.INFO [2022-10-18 23:50:56.773][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2022-10-18 23:50:56.775][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:56.777][biodb::testThat]
biodb.DEBUG[2022-10-18 23:50:56.783][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:50:56.790][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:56.792][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:56.797][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:50:57.506][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:50:58.124][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:50:58.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2022-10-18 23:50:58.164][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2022-10-18 23:50:58.202][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:50:58.204][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:50:58.206][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:58.208][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:50:58.210][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:58.212][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:50:58.214][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:50:58.216][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 23:50:58.218][biodb::testThat]
biodb.INFO [2022-10-18 23:50:58.220][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2022-10-18 23:50:58.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:58.224][biodb::testThat]
biodb.ERROR[2022-10-18 23:50:58.250][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-10-18 23:50:58.293][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-10-18 23:50:58.312][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 23:50:58.314][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-10-18 23:50:58.316][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-10-18 23:50:58.318][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 23:50:58.320][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:58.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:58.324][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.327][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 23:50:58.350][biodb::testContext]
biodb.INFO [2022-10-18 23:50:58.352][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:50:58.353][biodb::testContext] Test context - Test conversions
biodb.INFO [2022-10-18 23:50:58.355][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:50:58.357][biodb::testContext]
biodb.INFO [2022-10-18 23:50:58.366][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:50:58.369][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 23:50:58.377][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:50:58.380][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 23:50:58.382][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 23:50:58.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.390][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 23:50:58.392][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 23:50:58.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.401][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 23:50:58.402][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 23:50:58.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.410][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 23:50:58.412][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 23:50:58.414][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 23:50:58.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.418][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[2022-10-18 23:50:58.420][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 23:50:58.422][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 23:50:58.424][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 23:50:58.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.432][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 23:50:58.434][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 23:50:58.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.441][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 23:50:58.443][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 23:50:58.445][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 23:50:58.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.451][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 23:50:58.453][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 23:50:58.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.459][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[2022-10-18 23:50:58.461][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 23:50:58.463][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 23:50:58.465][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 23:50:58.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.473][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:50:58.475][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 23:50:58.476][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 23:50:58.478][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 23:50:58.480][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 23:50:58.482][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 23:50:58.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.487][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[2022-10-18 23:50:58.488][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 23:50:58.489][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 23:50:58.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.494][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 23:50:58.496][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 23:50:58.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.502][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 23:50:58.504][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 23:50:58.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.511][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 23:50:58.513][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 23:50:58.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.520][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 23:50:58.523][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 23:50:58.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.529][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:50:58.531][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 23:50:58.542][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-10-18 23:50:58.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.547][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[2022-10-18 23:50:58.549][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 23:50:58.552][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 23:50:58.554][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 23:50:58.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.560][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 23:50:58.563][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.565][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 23:50:58.568][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.570][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:58.572][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.574][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.576][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.578][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.580][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:50:58.582][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:58.584][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.586][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 23:50:58.588][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:58.590][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.592][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.594][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:50:58.594][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:50:58.594][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:50:58.594][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:50:58.594][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:50:58.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:50:58.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:58.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:58.602][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:58.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:58.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:58.608][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.610][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.612][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:58.614][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:58.616][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.618][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.620][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 23:50:58.624][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.626][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:50:58.628][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.630][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:58.632][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.634][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.636][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.638][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.640][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:50:58.642][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:58.644][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.646][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 23:50:58.648][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:58.650][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.652][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.654][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:50:58.654][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:50:58.654][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:50:58.654][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:50:58.654][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:50:58.655][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:50:58.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:58.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:58.661][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:58.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:58.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:58.666][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.667][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:58.671][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:58.673][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.674][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.676][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 23:50:58.680][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.682][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 23:50:58.684][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.686][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:58.687][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.689][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.691][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.693][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.694][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:50:58.696][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:58.697][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.699][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 23:50:58.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:58.703][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.705][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.707][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.708][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:50:58.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:58.711][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:58.712][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:58.714][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:58.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:58.718][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.719][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.721][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:58.723][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:58.725][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.727][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.730][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 23:50:58.733][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.736][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:50:58.738][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.740][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:58.742][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.744][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.746][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.748][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.750][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:50:58.751][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:58.753][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.754][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 23:50:58.755][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:58.757][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.758][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:58.760][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.762][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:50:58.763][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:58.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:58.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:58.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:58.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:58.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:58.774][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.776][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:58.778][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:58.780][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:58.782][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:50:58.784][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:50:58.786][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.787][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[2022-10-18 23:50:58.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.797][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[2022-10-18 23:50:58.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.805][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[2022-10-18 23:50:58.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.859][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[2022-10-18 23:50:58.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.868][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.DEBUG[2022-10-18 23:50:58.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.906][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[2022-10-18 23:50:58.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.921][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[2022-10-18 23:50:58.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:58.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:58.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:58.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:58.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:58.948][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 23:50:58.951][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 23:50:58.954][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 23:50:58.957][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 23:50:58.960][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:50:58.963][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 23:50:58.966][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 23:50:58.969][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 23:50:58.973][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 23:50:58.976][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 23:50:58.978][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:50:58.982][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 23:50:58.985][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 23:50:58.988][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 23:50:58.991][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 23:50:58.994][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:50:58.997][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 23:50:59.000][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 23:50:59.003][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:50:59.006][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 23:50:59.010][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 23:50:59.013][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 23:50:59.016][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 23:50:59.020][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 23:50:59.022][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 23:50:59.026][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 23:50:59.028][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 23:50:59.032][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 23:50:59.034][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 23:50:59.037][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 23:50:59.039][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 23:50:59.042][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 23:50:59.044][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 23:50:59.047][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 23:50:59.049][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 23:50:59.052][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 23:50:59.054][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 23:50:59.057][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 23:50:59.059][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 23:50:59.063][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 23:50:59.066][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 23:50:59.069][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 23:50:59.072][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 23:50:59.076][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 23:50:59.079][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 23:50:59.082][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 23:50:59.085][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 23:50:59.088][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 23:50:59.091][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 23:50:59.094][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 23:50:59.097][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 23:50:59.100][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 23:50:59.103][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 23:50:59.106][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 23:50:59.109][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 23:50:59.112][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 23:50:59.114][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 23:50:59.117][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 23:50:59.120][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 23:50:59.123][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 23:50:59.126][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 23:50:59.129][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 23:50:59.132][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 23:50:59.135][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 23:50:59.138][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 23:50:59.140][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 23:50:59.142][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:50:59.145][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:50:59.147][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 23:50:59.149][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 23:50:59.152][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 23:50:59.154][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 23:50:59.157][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 23:50:59.160][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 23:50:59.163][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 23:50:59.167][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 23:50:59.170][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 23:50:59.173][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 23:50:59.176][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 23:50:59.179][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 23:50:59.182][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 23:50:59.186][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 23:50:59.189][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 23:50:59.192][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 23:50:59.196][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:50:59.197][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:50:59.199][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.203][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.205][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[2022-10-18 23:50:59.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.244][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[2022-10-18 23:50:59.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.296][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[2022-10-18 23:50:59.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.417][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[2022-10-18 23:50:59.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:50:59.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:50:59.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:50:59.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:50:59.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:50:59.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:50:59.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:50:59.430][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-10-18 23:50:59.433][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-10-18 23:50:59.438][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:59.440][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 23:50:59.442][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:59.444][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:50:59.446][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:59.448][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:50:59.450][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:59.452][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-10-18 23:50:59.454][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 23:50:59.456][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:50:59.458][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:59.460][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-10-18 23:50:59.462][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-10-18 23:50:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-10-18 23:50:59.467][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 23:50:59.469][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:50:59.469][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:50:59.469][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:50:59.471][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 23:50:59.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:59.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:59.476][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:50:59.478][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:50:59.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:50:59.482][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:50:59.484][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:50:59.484][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-10-18 23:50:59.487][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:50:59.489][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:50:59.491][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 23:50:59.493][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-10-18 23:50:59.493][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-10-18 23:50:59.496][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:50:59.499][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:50:59.503][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-10-18 23:50:59.506][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:50:59.509][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:50:59.513][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:50:59.520][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-10-18 23:50:59.522][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-10-18 23:50:59.524][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-10-18 23:50:59.527][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-10-18 23:50:59.530][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 23:50:59.532][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 23:50:59.535][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-10-18 23:50:59.537][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-10-18 23:50:59.540][biodb::testThat]
biodb.INFO [2022-10-18 23:50:59.542][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2022-10-18 23:50:59.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:50:59.545][biodb::testThat]
biodb.DEBUG[2022-10-18 23:50:59.552][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.INFO [2022-10-18 23:50:59.571][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2022-10-18 23:50:59.574][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:50:59.576][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:50:59.578][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2022-10-18 23:51:00.019][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2022-10-18 23:51:00.600][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:00.615][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2022-10-18 23:51:00.639][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2022-10-18 23:51:00.651][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[2022-10-18 23:51:00.659][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:00.661][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:00.665][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:51:01.117][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:51:01.581][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:01.597][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2022-10-18 23:51:01.621][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2022-10-18 23:51:01.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:01.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:01.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:01.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:01.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:01.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:01.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:01.651][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:51:01.657][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:01.659][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:01.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:51:02.107][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:51:02.583][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:02.598][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2022-10-18 23:51:02.623][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2022-10-18 23:51:02.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:02.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:02.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:02.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:02.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:02.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:02.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:02.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:02.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:02.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:02.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:02.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:02.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:02.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:02.713][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[2022-10-18 23:51:02.720][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:51:02.722][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2022-10-18 23:51:02.725][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:51:02.728][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2022-10-18 23:51:02.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:02.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:02.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:02.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:02.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:02.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:02.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:02.753][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[2022-10-18 23:51:02.761][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:51:02.764][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2022-10-18 23:51:02.767][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:51:02.770][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2022-10-18 23:51:02.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:02.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:02.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:02.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:02.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:02.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:02.790][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[2022-10-18 23:51:02.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:02.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:02.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:02.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:02.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:02.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:02.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:02.847][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[2022-10-18 23:51:02.854][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:51:02.857][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2022-10-18 23:51:02.860][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:51:02.862][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2022-10-18 23:51:02.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:02.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:02.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:02.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:02.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:02.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:02.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:02.889][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[2022-10-18 23:51:02.896][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:51:02.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2022-10-18 23:51:02.901][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:51:02.904][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2022-10-18 23:51:02.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:02.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:02.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:02.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:02.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:02.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:02.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:02.930][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[2022-10-18 23:51:02.937][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:02.939][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:02.943][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:51:03.399][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:51:03.885][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:03.902][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2022-10-18 23:51:03.929][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2022-10-18 23:51:03.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:03.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:03.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:03.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:03.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:03.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:03.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 23:51:03.966][biodb::testThat]
biodb.INFO [2022-10-18 23:51:03.968][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2022-10-18 23:51:03.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:51:03.972][biodb::testThat]
biodb.DEBUG[2022-10-18 23:51:03.979][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:51:03.986][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:03.988][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:03.993][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:51:04.507][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:51:04.986][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:05.001][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2022-10-18 23:51:05.027][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2022-10-18 23:51:05.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:05.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:05.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:05.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:05.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:05.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:05.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:05.064][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[2022-10-18 23:51:05.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:05.074][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:05.077][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:51:05.518][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:51:05.981][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:05.995][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2022-10-18 23:51:06.020][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2022-10-18 23:51:06.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:06.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 23:51:06.052][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 23:51:06.054][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-10-18 23:51:06.056][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-10-18 23:51:06.058][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 23:51:06.060][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.063][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.067][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 23:51:06.074][biodb::testContext]
biodb.INFO [2022-10-18 23:51:06.101][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:51:06.103][biodb::testContext] Test context - Test web services
biodb.INFO [2022-10-18 23:51:06.105][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:51:06.107][biodb::testContext]
biodb.INFO [2022-10-18 23:51:06.116][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:51:06.119][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 23:51:06.126][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:51:06.128][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 23:51:06.130][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 23:51:06.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.137][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 23:51:06.139][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 23:51:06.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.146][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 23:51:06.148][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 23:51:06.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.154][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 23:51:06.156][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 23:51:06.157][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 23:51:06.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.163][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 23:51:06.164][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 23:51:06.165][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 23:51:06.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.172][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 23:51:06.174][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 23:51:06.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.180][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 23:51:06.182][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 23:51:06.184][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 23:51:06.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.190][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 23:51:06.192][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 23:51:06.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.199][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 23:51:06.201][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 23:51:06.202][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 23:51:06.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.208][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:51:06.210][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 23:51:06.211][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 23:51:06.213][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 23:51:06.214][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 23:51:06.216][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 23:51:06.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.222][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 23:51:06.225][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 23:51:06.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.230][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 23:51:06.233][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 23:51:06.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.241][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 23:51:06.243][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 23:51:06.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.249][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[2022-10-18 23:51:06.251][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 23:51:06.252][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 23:51:06.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.260][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 23:51:06.262][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 23:51:06.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.270][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:51:06.272][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 23:51:06.282][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-10-18 23:51:06.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.288][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 23:51:06.290][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 23:51:06.292][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 23:51:06.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.301][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 23:51:06.305][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.307][self$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[2022-10-18 23:51:06.309][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.311][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:06.312][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.313][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.314][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.316][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.317][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:51:06.318][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:06.319][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.321][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 23:51:06.323][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:06.324][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.326][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.328][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:51:06.328][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:51:06.328][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:51:06.328][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:51:06.328][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:51:06.330][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:51:06.332][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:06.334][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:06.336][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:06.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:06.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:06.342][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.344][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.346][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:06.347][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:06.348][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.349][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.351][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 23:51:06.354][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.356][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:51:06.358][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.360][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:06.362][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.363][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.365][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.367][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.368][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:51:06.370][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:06.372][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.374][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 23:51:06.375][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:06.377][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.379][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.381][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:51:06.381][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:51:06.381][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:51:06.381][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:51:06.381][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:51:06.383][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:51:06.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:06.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:06.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:06.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:06.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:06.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.395][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.397][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:06.399][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:06.401][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.403][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.405][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 23:51:06.409][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.411][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 23:51:06.413][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.415][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:06.418][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.420][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.422][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.424][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.426][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:51:06.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:06.430][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.432][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 23:51:06.433][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:06.434][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.436][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.438][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.440][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:51:06.443][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:06.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:06.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:06.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:06.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:06.452][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.454][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.457][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:06.459][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:06.460][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.462][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.465][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 23:51:06.469][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.471][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:51:06.473][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.475][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:06.478][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.480][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.482][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.484][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.486][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:51:06.488][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:06.491][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.493][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 23:51:06.495][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:06.497][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.499][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:06.501][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.503][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:51:06.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:06.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:06.509][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:06.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:06.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:06.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:06.518][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.520][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:06.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:06.524][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:06.526][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:06.528][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:51:06.530][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.551][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[2022-10-18 23:51:06.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.576][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[2022-10-18 23:51:06.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.584][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.DEBUG[2022-10-18 23:51:06.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.621][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[2022-10-18 23:51:06.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.633][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.DEBUG[2022-10-18 23:51:06.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.663][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[2022-10-18 23:51:06.665][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 23:51:06.668][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 23:51:06.671][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 23:51:06.673][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 23:51:06.675][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:51:06.677][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 23:51:06.678][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 23:51:06.681][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 23:51:06.684][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 23:51:06.685][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 23:51:06.687][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:51:06.698][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 23:51:06.701][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 23:51:06.703][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 23:51:06.705][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 23:51:06.708][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:51:06.711][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 23:51:06.714][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 23:51:06.717][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:51:06.720][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 23:51:06.723][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 23:51:06.726][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 23:51:06.729][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 23:51:06.732][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 23:51:06.735][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 23:51:06.738][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 23:51:06.741][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 23:51:06.745][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 23:51:06.747][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 23:51:06.750][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 23:51:06.752][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 23:51:06.755][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 23:51:06.757][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 23:51:06.759][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 23:51:06.761][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 23:51:06.764][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 23:51:06.767][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 23:51:06.770][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 23:51:06.772][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 23:51:06.775][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 23:51:06.778][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 23:51:06.781][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 23:51:06.784][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 23:51:06.787][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 23:51:06.789][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 23:51:06.791][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 23:51:06.794][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 23:51:06.798][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 23:51:06.800][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 23:51:06.803][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 23:51:06.806][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 23:51:06.809][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 23:51:06.812][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 23:51:06.815][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 23:51:06.818][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 23:51:06.821][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 23:51:06.823][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 23:51:06.825][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 23:51:06.829][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 23:51:06.832][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 23:51:06.835][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 23:51:06.837][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 23:51:06.840][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 23:51:06.843][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 23:51:06.846][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 23:51:06.849][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 23:51:06.852][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:51:06.855][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:51:06.857][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 23:51:06.860][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 23:51:06.863][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 23:51:06.865][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 23:51:06.867][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 23:51:06.870][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 23:51:06.873][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 23:51:06.875][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 23:51:06.878][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 23:51:06.881][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 23:51:06.884][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 23:51:06.887][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 23:51:06.890][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 23:51:06.893][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 23:51:06.896][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 23:51:06.899][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 23:51:06.901][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:51:06.903][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:51:06.905][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.909][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.921][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[2022-10-18 23:51:06.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.943][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[2022-10-18 23:51:06.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.953][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[2022-10-18 23:51:06.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.963][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[2022-10-18 23:51:06.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:06.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:06.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:06.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:06.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:06.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:06.996][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[2022-10-18 23:51:06.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:06.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:07.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:07.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:07.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:07.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:07.008][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[2022-10-18 23:51:07.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:07.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:07.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:07.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:07.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:07.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:07.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:07.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:07.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:07.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:07.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:07.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:07.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:07.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:07.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:07.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:07.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:07.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:07.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:07.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:07.044][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[2022-10-18 23:51:07.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:07.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:07.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:07.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:07.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:07.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:07.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:07.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:07.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:07.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:07.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:07.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:07.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:07.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:07.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:07.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:07.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:07.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:07.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:07.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:07.080][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.DEBUG[2022-10-18 23:51:07.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:07.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:07.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:07.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:07.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:07.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:07.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:07.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:07.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:07.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:07.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:07.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:07.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:07.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:07.108][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-10-18 23:51:07.111][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-10-18 23:51:07.115][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:07.118][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 23:51:07.120][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:07.122][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:07.124][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:07.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:07.128][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:07.130][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-10-18 23:51:07.132][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 23:51:07.134][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:07.136][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:07.138][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-10-18 23:51:07.139][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-10-18 23:51:07.141][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-10-18 23:51:07.144][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:07.145][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:51:07.145][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:51:07.145][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:51:07.147][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 23:51:07.148][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:07.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:07.152][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:07.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:07.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:07.157][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:07.159][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:51:07.159][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-10-18 23:51:07.161][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:07.163][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:07.165][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:07.167][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-10-18 23:51:07.167][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-10-18 23:51:07.170][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:51:07.173][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:51:07.177][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-10-18 23:51:07.180][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:51:07.183][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:51:07.187][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:51:07.193][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-10-18 23:51:07.195][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-10-18 23:51:07.198][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-10-18 23:51:07.200][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-10-18 23:51:07.202][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 23:51:07.203][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 23:51:07.205][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-10-18 23:51:07.206][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-10-18 23:51:07.209][biodb::testThat]
biodb.INFO [2022-10-18 23:51:07.211][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2022-10-18 23:51:07.213][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:51:07.215][biodb::testThat]
biodb.DEBUG[2022-10-18 23:51:07.220][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-10-18 23:51:07.226][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:51:07.228][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-10-18 23:51:07.231][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:51:07.234][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-10-18 23:51:07.238][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 23:51:07.245][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:07.247][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:07.250][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-10-18 23:51:07.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-10-18 23:51:08.172][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:08.188][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2022-10-18 23:51:08.211][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2022-10-18 23:51:08.222][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 23:51:08.224][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-10-18 23:51:08.227][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-10-18 23:51:08.229][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 23:51:08.230][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:08.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:08.234][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.236][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.238][FUN] Functions in observer BiodbConfig: [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 [2022-10-18 23:51:08.246][biodb::testContext]
biodb.INFO [2022-10-18 23:51:08.247][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:51:08.250][biodb::testContext] Test context - Non regression tests
biodb.INFO [2022-10-18 23:51:08.251][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 23:51:08.253][biodb::testContext]
biodb.INFO [2022-10-18 23:51:08.259][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:51:08.262][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 23:51:08.270][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:51:08.272][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 23:51:08.274][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 23:51:08.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.282][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 23:51:08.284][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 23:51:08.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.290][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 23:51:08.292][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 23:51:08.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.299][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 23:51:08.302][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 23:51:08.304][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 23:51:08.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.311][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 23:51:08.313][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 23:51:08.315][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 23:51:08.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.322][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 23:51:08.323][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 23:51:08.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.328][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 23:51:08.329][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 23:51:08.331][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 23:51:08.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.338][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 23:51:08.340][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 23:51:08.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.347][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 23:51:08.349][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 23:51:08.350][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 23:51:08.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.358][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:51:08.361][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 23:51:08.363][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 23:51:08.365][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 23:51:08.367][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 23:51:08.369][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 23:51:08.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.374][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[2022-10-18 23:51:08.376][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 23:51:08.378][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 23:51:08.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.386][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 23:51:08.389][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 23:51:08.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.395][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[2022-10-18 23:51:08.397][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 23:51:08.399][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 23:51:08.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.407][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 23:51:08.409][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 23:51:08.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.414][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[2022-10-18 23:51:08.416][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 23:51:08.418][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 23:51:08.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.425][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 23:51:08.427][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 23:51:08.438][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-10-18 23:51:08.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.444][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[2022-10-18 23:51:08.446][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 23:51:08.447][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 23:51:08.449][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 23:51:08.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.457][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 23:51:08.460][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.462][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 23:51:08.463][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.466][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:08.468][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.470][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.472][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.475][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.477][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:51:08.479][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:08.481][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.483][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 23:51:08.485][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:08.487][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.490][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.492][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:51:08.492][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:51:08.492][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:51:08.492][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:51:08.492][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:51:08.494][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:51:08.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:08.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:08.500][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:08.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:08.504][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:08.506][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.508][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.510][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:08.511][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:08.513][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.515][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.517][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 23:51:08.521][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.523][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:51:08.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.527][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:08.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.531][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.533][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.537][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:51:08.539][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:08.541][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.543][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 23:51:08.545][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:08.547][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.549][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.551][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:51:08.551][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:51:08.551][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:51:08.551][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 23:51:08.551][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 23:51:08.553][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:51:08.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:08.557][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:08.559][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:08.561][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:08.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:08.564][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.566][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.568][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:08.570][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:08.572][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.574][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.575][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 23:51:08.579][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.581][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 23:51:08.583][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.585][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:08.587][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.590][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.592][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.594][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.596][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 23:51:08.598][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:08.601][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.603][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 23:51:08.605][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:08.607][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.609][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.611][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.613][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:51:08.615][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:08.617][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:08.619][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:08.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:08.623][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:08.625][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.627][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.629][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:08.631][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:08.632][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.635][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.637][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 23:51:08.641][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.643][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 23:51:08.646][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:08.650][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.652][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.654][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.656][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.658][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 23:51:08.660][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:08.662][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.664][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 23:51:08.667][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:08.669][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.671][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:08.673][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.676][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 23:51:08.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:08.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:08.682][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:08.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:08.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:08.688][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:08.690][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:08.694][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:08.696][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:08.698][self$setPropertyValue]
biodb.DEBUG[2022-10-18 23:51:08.701][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:51:08.703][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.704][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[2022-10-18 23:51:08.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.713][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[2022-10-18 23:51:08.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.792][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[2022-10-18 23:51:08.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.859][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[2022-10-18 23:51:08.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.868][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.DEBUG[2022-10-18 23:51:08.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:08.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:08.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:08.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:08.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:08.878][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 23:51:08.881][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 23:51:08.884][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 23:51:08.887][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 23:51:08.890][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:51:08.893][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 23:51:08.896][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 23:51:08.899][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 23:51:08.902][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 23:51:08.905][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 23:51:08.908][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:51:08.911][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 23:51:08.914][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 23:51:08.917][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 23:51:08.921][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 23:51:08.924][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 23:51:08.927][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 23:51:08.930][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 23:51:08.932][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:51:08.936][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 23:51:08.938][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 23:51:08.942][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 23:51:08.945][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 23:51:08.947][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 23:51:08.950][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 23:51:08.953][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 23:51:08.956][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 23:51:08.959][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 23:51:08.962][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 23:51:08.965][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 23:51:08.968][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 23:51:08.972][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 23:51:08.975][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 23:51:08.978][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 23:51:08.981][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 23:51:08.984][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 23:51:08.987][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 23:51:08.991][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 23:51:08.994][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 23:51:08.997][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 23:51:09.000][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 23:51:09.002][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 23:51:09.005][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 23:51:09.008][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 23:51:09.011][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 23:51:09.014][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 23:51:09.017][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 23:51:09.020][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 23:51:09.024][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 23:51:09.027][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 23:51:09.030][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 23:51:09.034][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 23:51:09.037][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 23:51:09.040][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 23:51:09.043][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 23:51:09.046][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 23:51:09.049][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 23:51:09.052][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 23:51:09.055][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 23:51:09.058][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 23:51:09.060][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 23:51:09.063][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 23:51:09.066][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 23:51:09.069][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 23:51:09.072][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 23:51:09.075][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 23:51:09.078][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:51:09.081][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:51:09.084][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 23:51:09.087][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 23:51:09.089][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 23:51:09.092][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 23:51:09.095][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 23:51:09.098][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 23:51:09.101][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 23:51:09.104][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 23:51:09.108][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 23:51:09.111][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 23:51:09.114][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 23:51:09.117][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 23:51:09.120][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 23:51:09.123][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 23:51:09.126][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 23:51:09.129][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 23:51:09.133][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 23:51:09.135][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 23:51:09.136][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.139][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.168][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[2022-10-18 23:51:09.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.246][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[2022-10-18 23:51:09.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 23:51:09.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.357][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-10-18 23:51:09.360][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-10-18 23:51:09.363][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:09.365][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 23:51:09.367][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:09.370][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 23:51:09.372][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:09.374][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 23:51:09.376][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:09.378][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-10-18 23:51:09.380][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 23:51:09.382][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 23:51:09.385][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:09.387][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-10-18 23:51:09.389][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-10-18 23:51:09.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-10-18 23:51:09.393][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 23:51:09.395][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 23:51:09.395][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 23:51:09.395][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 23:51:09.397][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 23:51:09.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:09.402][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:09.404][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 23:51:09.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 23:51:09.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 23:51:09.410][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 23:51:09.412][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:51:09.412][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-10-18 23:51:09.414][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 23:51:09.415][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 23:51:09.417][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 23:51:09.419][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-10-18 23:51:09.419][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-10-18 23:51:09.421][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 23:51:09.425][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 23:51:09.449][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-10-18 23:51:09.453][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 23:51:09.456][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 23:51:09.461][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 23:51:09.468][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-10-18 23:51:09.471][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-10-18 23:51:09.473][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-10-18 23:51:09.476][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-10-18 23:51:09.479][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 23:51:09.481][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 23:51:09.484][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-10-18 23:51:09.486][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-10-18 23:51:09.489][biodb::testThat]
biodb.INFO [2022-10-18 23:51:09.491][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2022-10-18 23:51:09.493][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 23:51:09.495][biodb::testThat]
biodb.DEBUG[2022-10-18 23:51:09.501][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-10-18 23:51:09.508][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:51:09.510][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-10-18 23:51:09.513][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:51:09.516][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-10-18 23:51:09.523][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[2022-10-18 23:51:09.530][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 23:51:09.533][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2022-10-18 23:51:09.535][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 23:51:09.538][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2022-10-18 23:51:09.545][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2022-10-18 23:51:09.547][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 23:51:09.551][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2022-10-18 23:51:09.554][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 23:51:09.557][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 23:51:09.560][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 23:51:09.562][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 23:51:09.565][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 23:51:09.567][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 23:51:09.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:09.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:09.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:09.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:09.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:09.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:09.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 23:51:09.597][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2022-10-18 23:51:09.603][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 23:51:09.605][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 23:51:09.608][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2022-10-18 23:51:10.054][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2022-10-18 23:51:10.797][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 23:51:10.814][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2022-10-18 23:51:10.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2022-10-18 23:51:10.862][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2022-10-18 23:51:10.871][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 23:51:10.902][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 23:51:10.903][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 23:51:10.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 23:51:10.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:10.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:10.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:10.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:10.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:10.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 23:51:10.930][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:10.932][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:10.934][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:10.936][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:10.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:10.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:10.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:10.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:10.952][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:51:10.954][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:51:10.956][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:10.958][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:10.960][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 23:51:10.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 23:51:10.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:10.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:10.975][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:51:10.978][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:51:10.980][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:10.982][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:10.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 23:51:10.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 23:51:10.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:10.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:10.998][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 23:51:10.999][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 23:51:11.001][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.003][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.006][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 23:51:11.008][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 23:51:11.010][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.012][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.014][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:51:11.016][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:51:11.018][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.019][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.021][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:51:11.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 23:51:11.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.033][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:51:11.036][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:51:11.038][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.040][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.042][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 23:51:11.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 23:51:11.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.055][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:11.058][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:11.060][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.062][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:11.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 23:51:11.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.079][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:11.081][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:11.083][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.085][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 23:51:11.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 23:51:11.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.103][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:51:11.105][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:51:11.107][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.109][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.112][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 23:51:11.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 23:51:11.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.126][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:51:11.128][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:51:11.131][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.133][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.136][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 23:51:11.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 23:51:11.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:51:11.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:51:11.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:51:11.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:51:11.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:11.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:11.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 23:51:11.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 23:51:11.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:11.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:11.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:11.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:11.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:11.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:11.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:11.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:11.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:11.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:11.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 23:51:11.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 23:51:11.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 23:51:11.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 23:51:11.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 23:51:11.250][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2022-10-18 23:51:11.261][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 23:51:11.264][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-10-18 23:51:11.266][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-10-18 23:51:11.268][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 23:51:11.270][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 23:51:11.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 23:51:11.274][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 23:51:11.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 23:51:11.278][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 23:51:11.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
> 
> proc.time()
   user  system elapsed 
 43.080   1.177  84.596 

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn4.5470.7156.195
ChebiEntry0.8430.0150.871