Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:01 -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 nebbiolo1


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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biodbChebi_1.2.0.tar.gz
StartedAt: 2022-10-18 18:46:15 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:48:17 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 122.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biodbChebi_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/biodbChebi.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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-pc-linux-gnu (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 18:47:01.209][biodb::testContext]
biodb.INFO [2022-10-18 18:47:01.212][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:01.213][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-10-18 18:47:01.214][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:01.215][biodb::testContext]
biodb.INFO [2022-10-18 18:47:01.235][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:01.237][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:01.246][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:01.247][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:47:01.248][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:47:01.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.252][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:47:01.296][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:47:01.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.299][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 18:47:01.300][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:47:01.301][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:47:01.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.305][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:47:01.306][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:47:01.307][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:47:01.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.310][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 18:47:01.311][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:47:01.312][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:47:01.313][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:47:01.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.317][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:47:01.318][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:47:01.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.322][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:47:01.323][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:47:01.324][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:47:01.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.328][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:47:01.329][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:47:01.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.333][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:47:01.334][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:47:01.335][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:47:01.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.339][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:01.340][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:47:01.341][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:47:01.343][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:47:01.344][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:47:01.345][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:47:01.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.348][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 18:47:01.349][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:47:01.350][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:47:01.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.354][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:47:01.355][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:47:01.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.359][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:47:01.360][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:47:01.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.363][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:47:01.365][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:47:01.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.368][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:47:01.369][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:47:01.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.373][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:01.374][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:47:01.379][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:47:01.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.384][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:47:01.385][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:47:01.386][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:47:01.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.393][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:47:01.426][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.441][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 18:47:01.442][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.443][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:01.444][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.446][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.447][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.448][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:01.449][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:01.450][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.451][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:47:01.452][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:01.453][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.454][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.455][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:01.455][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:01.455][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:01.455][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:01.455][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:01.456][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:01.457][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.459][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:01.461][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.462][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.463][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.464][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.466][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:01.467][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:01.468][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.469][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.471][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:47:01.474][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.475][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:01.476][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.477][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:01.478][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.480][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.481][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.482][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:01.483][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:01.490][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.491][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:47:01.492][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:01.493][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.494][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.495][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:01.495][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:01.495][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:01.495][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:01.495][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:01.496][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:01.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.499][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:01.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.503][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:01.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:01.506][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.507][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.508][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:47:01.510][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.511][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 18:47:01.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.513][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:01.514][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.515][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.516][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.517][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.518][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:01.519][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:01.520][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.521][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:47:01.522][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:01.523][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.524][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.525][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.526][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:01.527][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.529][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:01.530][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.531][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.532][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.533][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.534][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:01.535][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:01.536][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.537][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.539][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:47:01.541][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.542][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:01.543][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.545][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:01.546][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.547][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.548][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.549][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.551][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:01.552][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:01.553][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.554][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:47:01.555][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:01.556][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.557][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.558][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.559][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:01.560][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.561][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:01.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.564][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.565][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.566][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:01.567][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:01.568][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.569][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:01.574][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:01.575][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.576][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 18:47:01.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.584][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 18:47:01.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.586][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 18:47:01.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.591][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 18:47:01.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.595][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 18:47:01.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.597][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 18:47:01.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.599][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 18:47:01.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.606][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 18:47:01.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.610][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 18:47:01.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.614][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 18:47:01.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.619][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 18:47:01.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.623][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 18:47:01.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.633][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 18:47:01.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.635][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 18:47:01.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.644][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 18:47:01.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.649][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 18:47:01.650][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:47:01.655][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:47:01.656][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:47:01.657][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:47:01.659][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:47:01.660][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:47:01.661][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:01.663][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:01.664][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:47:01.665][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:47:01.667][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:47:01.668][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:47:01.669][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:01.670][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:01.672][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:47:01.673][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:47:01.674][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:47:01.676][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:47:01.677][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:47:01.684][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:47:01.685][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:47:01.687][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:47:01.688][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:47:01.689][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:47:01.690][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:47:01.691][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:47:01.693][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:47:01.694][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:47:01.695][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:47:01.696][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:47:01.698][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:47:01.699][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:47:01.700][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:47:01.702][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:47:01.703][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:47:01.704][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:47:01.705][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:47:01.707][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:47:01.708][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:47:01.709][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:47:01.711][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:47:01.712][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:47:01.713][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:47:01.715][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:47:01.716][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:47:01.717][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:47:01.719][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:47:01.720][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:47:01.721][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:47:01.723][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:47:01.724][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:47:01.726][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:47:01.727][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:47:01.728][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:47:01.729][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:47:01.731][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:47:01.732][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:47:01.733][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:47:01.735][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:47:01.736][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:47:01.737][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:47:01.739][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:47:01.740][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:47:01.741][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:47:01.743][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:47:01.744][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:47:01.745][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:47:01.747][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:47:01.748][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:47:01.749][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:47:01.751][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:47:01.752][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:47:01.753][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:47:01.755][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:47:01.756][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:47:01.757][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:47:01.759][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:47:01.760][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:47:01.761][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:47:01.763][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:47:01.764][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:47:01.765][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:47:01.767][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:47:01.773][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:47:01.774][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:01.778][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:01.779][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.781][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.792][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 18:47:01.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.802][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 18:47:01.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.808][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 18:47:01.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.826][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 18:47:01.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.828][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 18:47:01.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.840][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 18:47:01.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.844][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 18:47:01.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.846][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 18:47:01.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.850][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 18:47:01.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.873][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 18:47:01.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:01.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:01.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:01.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:01.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:01.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:01.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:01.895][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:01.904][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-10-18 18:47:01.906][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.907][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.908][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.909][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:01.910][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.911][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.912][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.913][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-10-18 18:47:01.914][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 18:47:01.915][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:01.916][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.917][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-10-18 18:47:01.918][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-10-18 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-10-18 18:47:01.919][self$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 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-10-18 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-10-18 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-10-18 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-10-18 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-10-18 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-10-18 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-10-18 18:47:01.919][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-10-18 18:47:01.920][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:01.921][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:01.921][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:01.921][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:01.922][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 18:47:01.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.925][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:01.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:01.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:01.929][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:01.930][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:01.930][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-10-18 18:47:01.931][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:01.932][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:01.933][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:01.934][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-10-18 18:47:01.934][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-10-18 18:47:01.940][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:47:01.941][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:47:01.943][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-10-18 18:47:01.944][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:47:01.946][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:47:01.948][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:47:01.974][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-10-18 18:47:01.976][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-10-18 18:47:01.980][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-10-18 18:47:01.985][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-10-18 18:47:01.989][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:01.990][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:47:01.992][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-10-18 18:47:01.993][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-10-18 18:47:02.012][biodb::testThat]
biodb.INFO [2022-10-18 18:47:02.013][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-10-18 18:47:02.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:02.015][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:02.020][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.15-bioc/R/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2022-10-18 18:47:02.027][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:02.031][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:02.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:02.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:02.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:02.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:02.060][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 18:47:02.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:02.062][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.TRACE[2022-10-18 18:47:02.074][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.075][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.077][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.078][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.153][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:02.155][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:02.156][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.157][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.182][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:02.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:02.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.189][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:02.190][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:02.191][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.192][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.193][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:02.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:02.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.200][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.201][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.202][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.203][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.211][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.213][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.214][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.215][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.223][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.224][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.225][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.226][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.227][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.234][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:02.235][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.236][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.237][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.238][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:02.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.245][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.246][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.247][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.248][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.256][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:02.257][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:02.258][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.259][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:02.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:02.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.267][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:02.269][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.269][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.270][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.272][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:02.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.278][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:02.280][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:02.281][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.281][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:02.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:02.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:02.365][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2022-10-18 18:47:02.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.418][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:02.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:02.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.425][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:02.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:02.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.429][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:02.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:02.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.433][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:02.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:02.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.534][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.535][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.536][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.537][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.562][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.563][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.564][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.564][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:02.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:02.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:02.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:02.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:02.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:02.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:02.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.594][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:02.595][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:02.596][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.597][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:02.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:02.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.608][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:02.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:02.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.612][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:02.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:02.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.616][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:02.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:02.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.620][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:02.621][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:02.622][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.623][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.624][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:02.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:02.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.647][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.648][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.649][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.650][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.675][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.676][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.677][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.678][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.690][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:02.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:02.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.695][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:02.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:02.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.699][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:02.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:02.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.703][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:02.704][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:02.705][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.706][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.707][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:02.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:02.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.717][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.721][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.725][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.729][ef$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.730][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.731][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.732][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.733][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.749][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.753][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.757][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.761][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.762][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.763][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.764][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.765][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.777][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:02.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:02.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.782][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:02.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:02.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.786][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:02.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:02.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.791][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:02.792][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:02.793][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.794][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.795][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:02.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:02.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.821][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.822][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.823][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.824][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.851][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.853][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.854][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.855][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.869][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:02.870][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:02.871][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.872][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.878][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:02.879][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:02.880][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.881][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.887][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:02.889][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:02.890][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.891][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.897][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:02.898][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:02.899][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.900][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.907][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.916][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:02.917][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.918][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.924][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.926][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:02.927][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.928][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.933][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.935][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:02.936][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.937][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.943][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.944][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:02.945][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.946][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.952][ef$get] Asked field names are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.953][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:02.954][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.956][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.962][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:02.963][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:02.964][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.965][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:02.971][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:02.973][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:02.974][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:02.975][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:02.982][biodb::testThat]
biodb.INFO [2022-10-18 18:47:02.984][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-10-18 18:47:02.985][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:02.986][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:03.003][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2022-10-18 18:47:03.012][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:03.018][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2022-10-18 18:47:03.020][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:03.022][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2022-10-18 18:47:03.024][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:03.072][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:03.074][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:03.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:03.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:03.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:03.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:03.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:03.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:03.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:03.098][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.100][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.101][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.102][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.127][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:03.129][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:03.130][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.131][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.133][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:03.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:03.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.141][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:03.142][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:03.143][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.144][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.146][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:03.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:03.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.153][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:03.154][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:03.155][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.156][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:03.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:03.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.166][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:03.167][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:03.168][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.169][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:03.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:03.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.178][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:03.180][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:03.181][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.182][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.183][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:03.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:03.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.191][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:03.192][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:03.193][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.194][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.196][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:03.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:03.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.204][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:03.205][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:03.206][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.207][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:03.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:03.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.216][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:03.218][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:03.219][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.220][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.221][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:03.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:03.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.229][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:03.231][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:03.232][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.233][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.234][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:03.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:03.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.242][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:03.244][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:03.245][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.246][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.248][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:03.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:03.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:03.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:03.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:03.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:03.314][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2022-10-18 18:47:03.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-18 18:47:03.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-18 18:47:03.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-18 18:47:03.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-18 18:47:03.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-18 18:47:03.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-18 18:47:03.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:03.335][biodb::testThat]
biodb.INFO [2022-10-18 18:47:03.336][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-10-18 18:47:03.337][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:03.338][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:03.342][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:03.343][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:03.344][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.345][ef$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:03.347][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2022-10-18 18:47:03.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:03.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:03.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:03.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:03.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:03.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:03.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:03.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:03.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:03.391][function(conn, opt)] With value "squalene".
biodb.DEBUG[2022-10-18 18:47:03.406][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 18:47:03.435][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:03.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-10-18 18:47:03.453][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:03.455][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-10-18 18:47:03.479][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 18:47:03.483][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:03.484][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:03.486][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 18:47:07.107][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 18:47:07.669][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:07.682][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2022-10-18 18:47:07.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2022-10-18 18:47:07.744][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2022-10-18 18:47:07.766][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:07.768][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:07.770][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.772][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.774][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:07.775][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:07.777][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.778][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:07.782][biodb::testThat]
biodb.INFO [2022-10-18 18:47:07.783][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-10-18 18:47:07.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:07.786][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:07.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:07.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:07.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:07.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:07.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:07.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:07.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:07.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:07.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:07.973][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:07.980][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:07.982][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 18:47:07.985][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:07.987][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2022-10-18 18:47:08.015][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.017][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-10-18 18:47:08.019][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:08.021][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:08.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:08.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:08.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:08.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:08.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:08.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:08.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:08.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:08.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:08.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:08.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:08.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:08.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.102][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:08.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:08.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.130][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:08.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:08.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.134][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:08.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:08.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.139][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:08.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:08.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:08.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:08.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:08.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:08.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:08.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:08.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.186][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:08.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:08.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:08.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:08.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:08.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:08.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.200][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:08.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:08.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.204][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:08.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:08.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.209][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:08.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:08.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:08.213][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:08.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:08.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:08.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:08.221][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.223][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-10-18 18:47:08.224][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:08.225][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.232][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.233][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-10-18 18:47:08.234][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:08.235][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.242][biodb::testThat]
biodb.INFO [2022-10-18 18:47:08.243][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-10-18 18:47:08.244][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:08.245][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:08.250][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2022-10-18 18:47:08.869][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2022-10-18 18:47:10.127][biodb::testThat]
biodb.INFO [2022-10-18 18:47:10.129][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-10-18 18:47:10.130][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:10.132][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:10.581][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 18:47:11.036][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.038][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.040][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.041][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.043][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.044][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:11.045][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.047][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:11.052][biodb::testThat]
biodb.INFO [2022-10-18 18:47:11.053][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2022-10-18 18:47:11.055][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:11.056][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:11.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:11.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:11.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:11.190][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:11.194][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:11.196][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 18:47:11.197][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:11.199][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-10-18 18:47:11.291][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:11.295][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:11.297][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 18:47:11.299][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:11.302][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2022-10-18 18:47:11.328][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:11.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:11.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:11.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:11.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:11.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:11.414][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:11.430][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:11.432][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:11.446][private$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 18:47:11.860][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 18:47:12.289][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:12.313][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2022-10-18 18:47:12.332][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2022-10-18 18:47:12.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:12.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.353][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 18:47:12.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.356][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 18:47:12.358][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2022-10-18 18:47:12.423][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:12.425][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2022-10-18 18:47:12.427][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:12.428][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:12.429][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:12.430][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:12.431][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:12.432][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:12.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:12.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.452][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2022-10-18 18:47:12.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:12.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:12.457][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2022-10-18 18:47:12.899][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 18:47:13.341][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:13.349][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2022-10-18 18:47:13.361][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2022-10-18 18:47:13.374][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2022-10-18 18:47:13.380][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:13.409][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:13.411][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:13.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:13.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:13.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:13.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:13.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:13.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:13.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:13.426][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.428][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.429][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.430][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.439][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:13.440][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:13.441][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.443][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.444][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:13.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:13.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.453][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.454][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.455][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.456][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.458][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.466][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:13.467][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:13.468][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.469][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:13.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:13.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.479][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:13.480][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:13.481][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.482][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:13.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:13.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.492][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:13.493][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:13.494][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.495][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.496][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:13.497][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:13.498][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.500][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.501][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:13.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:13.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.509][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.510][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.511][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.512][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.520][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.522][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.523][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.524][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.538][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:13.539][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:13.540][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.541][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.543][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:13.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:13.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.551][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:13.552][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:13.553][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.554][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.556][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:13.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:13.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:13.612][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2022-10-18 18:47:13.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:13.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:13.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:13.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:13.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:13.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:13.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:13.636][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 18:47:13.639][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:13.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:13.642][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 18:47:14.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 18:47:15.953][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:15.965][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2022-10-18 18:47:15.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2022-10-18 18:47:16.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:16.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:16.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:16.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:16.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:16.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:16.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:16.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:16.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:16.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:16.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:16.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:16.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:16.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:16.064][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:16.068][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:16.069][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:16.071][private$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 18:47:16.496][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 18:47:16.937][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:16.948][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2022-10-18 18:47:16.966][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2022-10-18 18:47:17.046][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 18:47:17.055][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:17.058][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 18:47:17.060][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:17.062][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-10-18 18:47:17.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:17.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:17.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:17.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:17.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:17.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:17.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:17.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:17.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:17.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:17.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:17.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:17.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:17.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:17.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:17.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:17.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:17.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:17.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:17.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:17.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:17.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:17.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:17.117][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 18:47:17.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:17.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:17.120][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2022-10-18 18:47:17.121][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:17.122][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2022-10-18 18:47:17.124][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:17.125][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:17.126][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:17.127][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:17.128][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:17.129][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:17.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:17.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:17.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:17.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:17.152][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 18:47:17.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:17.154][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 18:47:17.155][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2022-10-18 18:47:17.164][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:17.165][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:17.167][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2022-10-18 18:47:17.613][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 18:47:18.046][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:18.059][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2022-10-18 18:47:18.078][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2022-10-18 18:47:18.097][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2022-10-18 18:47:18.104][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:18.133][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:18.136][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:18.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:18.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:18.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:18.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:18.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:18.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:18.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:18.173][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:18.175][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:18.176][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.177][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:18.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:18.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.189][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:18.191][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:18.192][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.193][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.195][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:18.197][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:18.198][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.199][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.201][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:18.203][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:18.204][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.206][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.207][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:18.209][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:18.210][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.211][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.213][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:18.215][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:18.217][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.218][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.220][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:18.221][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.223][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.224][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.226][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.228][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.229][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.231][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.232][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:18.234][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:18.236][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.237][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:18.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:18.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.265][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:18.268][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:18.269][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.270][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.272][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:18.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:18.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.281][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:18.283][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:18.284][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.285][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:18.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:18.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:18.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:18.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:18.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:18.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:18.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:18.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:18.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:18.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:18.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:18.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:18.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:18.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:18.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:18.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:18.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:18.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:18.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:18.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:18.366][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2022-10-18 18:47:18.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:18.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:18.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:18.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:18.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:18.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:18.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:18.403][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 18:47:18.404][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2022-10-18 18:47:18.405][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:18.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2022-10-18 18:47:18.409][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:18.410][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:18.411][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:18.412][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:18.413][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:18.414][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:18.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:18.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:18.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:18.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:18.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:18.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:18.428][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 18:47:18.430][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2022-10-18 18:47:18.433][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:18.434][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:18.435][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2022-10-18 18:47:18.858][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 18:47:19.318][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:19.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2022-10-18 18:47:19.349][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2022-10-18 18:47:19.366][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2022-10-18 18:47:19.373][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:19.400][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:19.402][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:19.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:19.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:19.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:19.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:19.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:19.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:19.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:19.425][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:19.426][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:19.427][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.428][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:19.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:19.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.438][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:19.439][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:19.441][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.442][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.444][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:19.445][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:19.446][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.447][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.449][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:19.451][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:19.452][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.453][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.455][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:19.456][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:19.457][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.458][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.460][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:19.461][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:19.462][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.463][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.465][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:19.466][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.467][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.474][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.477][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:19.479][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:19.480][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.481][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.483][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:19.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:19.484][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.485][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:19.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:19.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.495][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:19.496][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:19.497][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.498][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.499][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:19.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:19.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.506][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:19.508][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:19.509][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.510][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:19.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:19.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:19.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:19.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:19.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:19.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:19.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:19.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:19.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:19.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:19.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:19.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:19.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:19.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:19.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:19.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:19.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:19.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:19.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:19.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:19.555][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2022-10-18 18:47:19.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:19.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:19.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:19.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:19.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:19.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:19.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:19.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:19.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:19.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:19.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:19.595][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2022-10-18 18:47:19.596][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:19.598][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2022-10-18 18:47:19.599][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:19.600][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:19.601][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:19.602][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:19.603][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:19.604][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:19.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:19.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:19.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:19.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:19.614][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 18:47:19.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:19.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:19.617][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2022-10-18 18:47:19.620][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:19.621][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:19.622][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2022-10-18 18:47:20.038][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 18:47:20.560][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:20.572][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2022-10-18 18:47:20.592][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2022-10-18 18:47:20.610][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2022-10-18 18:47:20.629][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:20.654][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:20.656][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:20.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:20.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:20.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:20.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:20.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:20.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:20.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:20.676][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:20.678][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:20.679][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.680][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:20.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:20.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.692][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:20.694][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:20.695][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.697][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.698][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:20.700][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:20.701][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.703][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.705][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:20.706][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:20.708][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.709][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.712][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:20.714][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:20.716][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.719][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.721][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:20.723][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:20.724][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.725][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.726][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:20.727][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.728][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.729][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.730][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:20.732][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:20.732][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.733][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.735][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:20.736][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:20.737][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.737][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:20.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:20.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.746][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:20.748][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:20.749][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.749][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:20.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:20.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.758][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:20.759][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:20.760][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.761][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:20.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:20.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:20.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:20.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:20.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:20.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:20.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:20.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:20.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:20.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:20.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:20.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:20.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:20.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:20.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:20.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:20.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:20.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:20.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:20.810][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2022-10-18 18:47:20.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:20.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:20.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:20.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:20.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:20.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:20.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:20.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:20.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:20.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:20.840][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 18:47:20.841][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2022-10-18 18:47:20.842][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:20.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2022-10-18 18:47:20.845][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:20.846][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:20.847][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:20.849][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:20.850][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:20.851][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:20.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:20.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:20.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:20.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:20.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:20.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:20.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:20.865][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2022-10-18 18:47:20.867][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:20.868][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:20.870][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2022-10-18 18:47:21.337][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 18:47:21.776][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:21.787][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2022-10-18 18:47:21.804][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2022-10-18 18:47:21.820][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2022-10-18 18:47:21.826][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:21.849][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:21.851][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:21.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:21.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:21.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:21.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:21.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:21.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:21.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:21.872][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:21.874][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:21.876][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.877][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:21.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:21.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.896][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:21.897][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:21.898][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.899][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.900][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:21.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:21.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.907][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:21.908][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:21.909][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.910][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.911][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:21.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:21.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.918][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:21.919][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:21.920][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.921][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:21.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:21.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.929][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:21.930][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:21.931][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.932][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:21.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:21.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.940][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:21.941][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:21.942][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.943][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.945][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:21.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:21.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.952][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:21.953][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:21.953][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.954][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.956][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:21.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:21.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.963][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:21.964][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:21.965][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.966][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:21.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:21.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.974][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:21.975][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:21.976][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.977][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:21.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:21.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.986][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:21.987][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:21.988][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.989][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:21.990][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:21.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:21.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:21.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.002][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:22.004][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:22.005][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.006][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.008][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:22.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:22.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:22.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:22.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:22.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:22.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:22.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:22.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:22.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:22.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:22.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:22.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:22.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:22.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:22.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:22.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:22.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:22.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:22.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:22.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:22.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:22.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:22.059][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2022-10-18 18:47:22.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:22.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:22.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:22.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:22.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:22.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:22.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:22.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:22.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:22.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:22.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:22.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:22.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:22.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:22.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:22.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:22.083][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2022-10-18 18:47:22.084][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:22.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2022-10-18 18:47:22.087][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:22.088][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:22.089][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:22.090][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:22.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:22.092][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:22.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:22.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:22.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:22.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:22.103][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 18:47:22.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:22.105][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 18:47:22.106][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2022-10-18 18:47:22.109][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:22.110][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:22.117][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2022-10-18 18:47:22.530][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 18:47:22.967][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:22.974][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2022-10-18 18:47:22.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2022-10-18 18:47:22.996][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2022-10-18 18:47:23.000][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:23.015][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:23.017][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:23.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:23.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:23.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:23.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:23.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:23.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:23.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:23.042][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:23.043][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:23.044][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.045][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:23.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:23.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.053][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:23.054][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:23.055][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.056][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.057][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:23.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:23.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.065][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:23.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:23.067][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.068][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:23.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.077][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:23.078][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:23.079][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.080][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:23.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:23.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.089][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:23.090][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:23.091][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.092][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:23.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:23.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.101][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:23.102][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:23.103][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.104][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.105][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:23.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:23.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.112][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:23.113][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:23.114][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.115][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.116][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:23.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:23.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.124][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:23.125][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:23.126][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.127][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:23.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:23.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.135][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:23.136][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:23.137][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.138][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:23.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:23.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.146][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:23.148][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:23.154][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.155][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.157][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:23.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:23.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.164][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:23.165][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:23.165][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.166][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.168][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:23.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:23.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:23.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:23.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:23.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:23.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:23.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:23.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:23.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:23.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:23.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:23.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:23.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:23.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:23.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:23.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:23.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:23.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:23.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:23.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:23.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:23.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:23.220][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2022-10-18 18:47:23.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:23.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:23.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:23.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:23.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:23.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:23.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:23.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:23.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:23.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:23.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:23.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:23.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:23.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:23.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:23.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:23.246][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2022-10-18 18:47:23.248][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:23.249][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2022-10-18 18:47:23.251][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:23.252][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:23.253][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:23.254][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:23.255][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:23.256][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:23.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:23.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:23.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:23.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:23.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:23.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:23.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:23.277][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2022-10-18 18:47:23.280][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:23.281][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:23.282][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2022-10-18 18:47:23.709][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 18:47:24.160][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:24.167][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2022-10-18 18:47:24.178][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2022-10-18 18:47:24.189][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2022-10-18 18:47:24.193][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:24.220][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:24.221][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:24.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:24.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:24.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:24.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:24.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:24.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:24.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:24.236][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:24.237][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:24.238][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.239][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:24.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:24.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.247][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:24.248][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:24.249][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.250][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.252][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:24.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:24.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.259][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:24.260][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:24.261][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.262][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.263][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:24.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:24.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.271][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:24.272][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:24.273][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.274][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:24.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:24.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.283][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:24.284][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:24.285][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.286][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:24.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:24.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.295][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:24.296][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:24.297][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.298][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.299][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:24.301][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:24.301][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.302][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.304][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:24.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:24.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.311][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:24.312][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:24.313][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.314][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:24.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:24.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.323][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:24.324][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:24.325][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.326][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:24.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:24.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.344][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:24.345][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:24.346][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.347][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.349][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:24.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:24.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.356][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:24.357][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:24.358][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.359][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.360][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:24.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:24.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:24.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:24.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:24.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:24.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:24.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:24.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:24.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:24.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:24.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:24.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:24.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:24.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:24.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:24.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:24.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:24.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:24.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:24.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:24.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:24.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:24.411][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2022-10-18 18:47:24.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:24.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:24.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:24.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:24.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:24.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:24.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:24.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:24.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:24.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:24.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:24.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:24.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:24.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:24.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:24.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:24.438][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2022-10-18 18:47:24.439][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:24.441][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2022-10-18 18:47:24.443][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:24.444][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:24.445][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:24.446][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:24.447][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:24.449][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:24.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:24.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:24.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:24.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:24.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:24.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:24.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:24.470][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2022-10-18 18:47:24.473][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:24.474][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:24.475][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2022-10-18 18:47:24.895][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 18:47:27.295][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:27.306][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2022-10-18 18:47:27.324][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2022-10-18 18:47:27.341][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2022-10-18 18:47:27.346][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:27.545][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:27.547][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:27.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:27.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:27.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:27.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:27.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:27.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:27.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:27.561][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:27.562][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:27.563][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.564][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:27.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:27.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.572][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:27.573][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:27.574][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.575][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.576][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:27.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:27.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.583][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:27.584][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:27.585][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.586][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.588][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:27.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:27.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.595][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:27.596][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:27.596][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.597][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:27.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:27.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.606][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:27.607][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:27.608][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.609][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:27.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:27.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.618][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:27.619][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:27.620][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.621][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.623][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:27.624][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:27.625][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.625][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.627][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:27.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:27.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.634][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:27.635][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:27.636][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.637][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:27.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:27.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.645][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:27.646][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:27.647][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.648][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:27.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:27.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.656][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:27.657][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:27.658][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.659][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.661][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:27.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:27.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.668][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:27.669][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:27.670][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.671][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.673][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:27.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:27.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:27.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:27.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:27.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:27.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:27.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:27.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:27.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:27.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:27.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:27.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:27.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:27.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:27.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:27.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:27.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:27.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:27.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:27.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:27.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:27.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:27.734][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2022-10-18 18:47:27.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:27.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:27.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:27.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:27.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:27.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:27.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:27.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:27.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:27.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:27.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:27.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:27.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:27.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:27.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:27.761][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 18:47:27.763][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2022-10-18 18:47:27.764][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:27.766][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2022-10-18 18:47:27.767][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:27.769][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:27.770][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:27.771][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:27.772][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:27.773][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:27.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:27.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:27.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:27.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:27.787][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 18:47:27.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:27.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:27.790][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2022-10-18 18:47:27.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:27.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:27.796][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2022-10-18 18:47:28.220][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 18:47:28.662][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:28.670][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2022-10-18 18:47:28.683][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2022-10-18 18:47:28.695][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2022-10-18 18:47:28.699][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:28.718][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:28.719][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:28.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:28.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:28.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:28.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:28.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:28.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:28.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:28.749][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:28.751][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:28.752][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.752][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:28.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:28.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.761][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:28.762][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:28.763][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.764][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.766][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:28.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:28.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.773][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:28.774][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:28.775][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.776][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:28.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:28.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.784][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:28.785][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:28.786][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.787][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:28.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:28.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.795][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:28.796][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:28.797][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.797][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.799][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:28.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:28.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.805][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:28.806][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:28.807][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.808][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.809][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:28.811][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:28.811][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.812][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.814][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:28.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:28.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.820][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:28.821][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:28.822][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.823][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:28.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:28.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.831][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:28.832][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:28.833][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.834][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.835][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:28.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:28.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.842][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:28.843][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:28.844][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.845][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.846][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:28.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.854][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:28.855][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:28.856][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.857][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.858][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:28.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:28.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:28.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:28.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:28.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:28.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:28.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:28.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:28.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:28.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:28.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:28.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:28.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:28.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:28.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:28.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:28.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:28.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:28.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:28.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:28.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:28.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:28.909][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2022-10-18 18:47:28.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:28.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:28.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:28.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:28.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:28.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:28.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:28.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:28.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:28.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:28.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:28.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:28.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:28.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:28.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:28.932][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 18:47:28.933][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2022-10-18 18:47:28.934][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:28.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2022-10-18 18:47:28.937][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:28.938][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:28.939][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:28.940][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:28.941][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:28.942][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:28.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:28.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:28.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:28.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:28.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:28.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:28.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:28.955][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2022-10-18 18:47:28.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:28.958][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:28.960][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2022-10-18 18:47:29.373][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 18:47:29.801][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:29.809][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2022-10-18 18:47:29.820][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2022-10-18 18:47:29.831][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2022-10-18 18:47:29.836][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:29.851][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:29.852][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:29.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:29.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:29.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:29.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:29.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:29.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:29.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:29.872][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:29.877][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:29.879][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.880][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:29.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:29.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.888][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:29.889][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:29.890][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.891][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.892][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:29.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:29.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.899][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:29.900][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:29.901][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.902][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:29.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:29.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.911][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:29.912][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:29.913][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.914][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:29.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:29.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.922][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:29.923][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:29.924][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.925][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:29.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:29.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.933][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:29.934][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:29.935][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.936][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.937][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:29.938][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:29.939][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.940][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.941][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:29.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:29.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.948][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:29.949][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:29.950][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.951][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:29.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:29.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.959][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:29.961][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:29.962][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.963][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:29.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:29.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.971][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:29.972][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:29.973][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.974][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.976][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:29.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:29.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:29.984][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:29.985][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.986][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.987][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:29.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:29.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:29.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:29.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:29.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:29.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:30.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:30.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:30.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:30.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:30.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:30.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:30.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:30.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:30.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:30.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:30.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:30.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:30.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:30.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:30.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:30.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:30.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:30.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:30.037][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2022-10-18 18:47:30.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:30.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:30.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:30.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:30.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:30.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:30.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:30.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:30.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:30.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:30.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:30.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:30.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:30.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:30.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:30.058][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 18:47:30.060][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2022-10-18 18:47:30.060][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:30.062][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2022-10-18 18:47:30.063][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:30.064][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:30.065][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:30.066][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:30.067][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:30.068][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:30.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:30.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:30.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:30.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:30.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:30.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:30.080][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 18:47:30.081][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2022-10-18 18:47:30.084][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:30.085][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:30.086][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2022-10-18 18:47:30.502][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 18:47:30.938][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:30.950][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2022-10-18 18:47:30.966][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2022-10-18 18:47:30.983][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2022-10-18 18:47:30.989][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:31.013][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:31.015][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:31.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:31.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:31.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:31.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:31.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:31.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:31.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:31.037][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:31.039][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:31.041][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.043][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:31.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:31.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.065][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:31.067][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:31.067][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.068][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.070][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:31.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:31.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.076][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:31.077][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:31.078][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.079][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.080][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:31.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:31.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.087][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:31.088][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:31.089][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.090][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:31.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:31.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.097][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:31.098][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:31.099][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.100][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:31.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:31.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.108][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:31.109][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:31.110][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.111][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.112][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:31.113][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:31.114][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.114][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.116][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:31.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:31.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.122][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:31.123][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:31.124][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.125][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:31.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:31.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.132][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:31.133][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:31.134][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.135][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:31.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:31.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.143][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:31.144][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:31.145][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.146][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.147][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:31.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:31.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.154][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:31.155][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:31.155][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.156][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.157][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:31.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:31.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:31.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:31.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:31.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:31.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:31.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:31.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:31.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:31.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:31.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:31.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:31.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:31.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:31.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:31.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:31.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:31.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:31.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:31.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:31.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:31.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:31.206][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2022-10-18 18:47:31.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:31.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:31.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:31.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:31.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:31.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:31.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:31.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:31.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:31.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:31.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:31.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:31.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:31.227][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 18:47:31.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:31.229][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 18:47:31.230][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2022-10-18 18:47:31.231][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:31.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2022-10-18 18:47:31.234][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:31.235][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:31.236][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:31.237][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:31.238][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:31.239][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:31.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:31.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:31.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:31.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:31.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:31.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:31.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:31.252][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2022-10-18 18:47:31.255][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:31.256][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:31.257][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2022-10-18 18:47:34.671][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 18:47:35.266][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2022-10-18 18:47:35.271][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2022-10-18 18:47:35.277][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2022-10-18 18:47:35.290][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2022-10-18 18:47:35.302][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2022-10-18 18:47:35.307][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:35.327][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:35.329][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:35.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:35.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:35.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:35.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:35.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:35.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:35.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:35.346][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:35.347][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:35.348][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.349][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:35.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:35.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.358][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:35.360][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:35.361][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.362][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.363][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:35.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:35.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.382][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:35.384][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:35.385][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.386][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.387][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:35.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:35.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.394][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:35.396][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:35.396][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.397][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.399][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:35.400][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:35.401][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.402][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.403][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:35.405][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:35.406][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.407][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.408][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:35.410][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:35.411][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.412][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.414][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:35.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:35.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.423][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:35.424][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:35.425][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.427][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:35.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:35.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.436][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:35.437][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:35.438][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.439][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.440][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:35.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:35.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.448][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:35.449][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:35.450][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.451][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.453][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:35.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:35.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.461][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:35.463][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:35.464][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.465][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:35.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:35.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:35.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:35.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:35.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:35.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:35.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:35.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:35.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:35.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:35.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:35.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:35.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:35.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:35.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:35.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:35.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:35.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:35.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:35.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:35.512][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2022-10-18 18:47:35.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:35.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:35.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:35.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:35.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:35.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:35.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:35.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:35.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:35.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:35.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:35.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:35.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:35.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:35.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:35.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:35.543][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2022-10-18 18:47:35.545][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:35.547][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2022-10-18 18:47:35.549][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:35.550][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:35.552][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:35.553][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:35.555][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:35.557][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:35.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:35.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:35.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:35.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:35.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:35.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:35.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:35.579][scheduler$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 18:47:35.581][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:35.582][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:35.584][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2022-10-18 18:47:36.000][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2022-10-18 18:47:36.434][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:36.447][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2022-10-18 18:47:36.467][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2022-10-18 18:47:36.485][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2022-10-18 18:47:36.491][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:36.508][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:36.510][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:36.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:36.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:36.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:36.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:36.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:36.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:36.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:36.528][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:36.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:36.531][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.532][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:36.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:36.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.541][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:36.542][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:36.543][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.544][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.546][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:36.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:36.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.554][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:36.555][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:36.556][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.557][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.559][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:36.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:36.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.566][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:36.567][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:36.568][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.569][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.570][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:36.572][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:36.572][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.573][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.575][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:36.576][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:36.577][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.578][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.579][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:36.580][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:36.581][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.582][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.583][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:36.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:36.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.599][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:36.600][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:36.601][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.602][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:36.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:36.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.612][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:36.613][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:36.614][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.615][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:36.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:36.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.625][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:36.626][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:36.627][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.628][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.630][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:36.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:36.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.638][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:36.639][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:36.640][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.641][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:36.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:36.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:36.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:36.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:36.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:36.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:36.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:36.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:36.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:36.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:36.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:36.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:36.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:36.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:36.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:36.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:36.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:36.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:36.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:36.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:36.685][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2022-10-18 18:47:36.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:36.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:36.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:36.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:36.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:36.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:36.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:36.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:36.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:36.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:36.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:36.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:36.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:36.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:36.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:36.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:36.709][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2022-10-18 18:47:36.710][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:36.712][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2022-10-18 18:47:36.713][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:36.715][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:36.716][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:36.717][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:36.718][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:36.719][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:36.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:36.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:36.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:36.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:36.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:36.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:36.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:36.734][scheduler$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 18:47:36.737][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:36.738][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:36.739][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2022-10-18 18:47:37.156][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2022-10-18 18:47:37.598][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:37.609][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2022-10-18 18:47:37.626][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2022-10-18 18:47:37.643][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2022-10-18 18:47:37.650][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:37.675][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:37.677][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:37.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:37.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:37.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:37.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:37.694][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 18:47:37.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:37.698][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 18:47:37.703][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:37.705][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:37.707][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.708][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:37.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:37.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.715][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:37.716][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:37.717][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.718][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.719][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:37.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:37.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.725][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:37.726][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:37.727][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.728][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:37.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:37.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.735][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:37.736][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:37.737][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.738][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:37.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:37.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.746][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:37.747][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:37.748][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.748][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:37.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:37.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.756][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:37.757][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:37.758][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.759][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.760][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:37.761][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:37.762][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.763][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.764][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:37.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:37.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.771][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:37.772][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:37.773][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.773][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:37.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:37.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.809][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:37.811][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:37.812][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.813][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:37.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:37.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.822][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:37.823][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:37.824][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.825][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.826][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:37.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:37.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.834][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:37.835][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:37.836][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.837][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.838][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:37.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:37.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:37.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:37.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:37.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:37.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:37.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:37.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:37.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:37.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:37.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:37.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:37.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:37.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:37.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:37.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:37.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:37.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:37.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:37.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:37.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:37.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:37.889][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2022-10-18 18:47:37.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:37.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:37.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:37.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:37.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:37.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:37.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:37.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:37.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:37.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:37.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:37.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:37.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:37.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:37.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:37.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:37.914][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2022-10-18 18:47:37.915][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:37.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2022-10-18 18:47:37.918][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:37.920][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:37.921][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:37.922][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:37.924][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:37.925][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:37.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:37.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:37.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:37.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:37.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:37.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:37.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:37.941][scheduler$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 18:47:37.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:37.945][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:37.946][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2022-10-18 18:47:38.359][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2022-10-18 18:47:38.792][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:38.799][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2022-10-18 18:47:38.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2022-10-18 18:47:38.821][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2022-10-18 18:47:38.825][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:38.840][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:38.841][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:38.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:38.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:38.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:38.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:38.851][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 18:47:38.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:38.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:38.855][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:38.856][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:38.857][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.858][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:38.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:38.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.866][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:38.867][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:38.868][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.869][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.870][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:38.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:38.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.877][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:38.878][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:38.879][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.880][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.881][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:38.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:38.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.887][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:38.889][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:38.889][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.890][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:38.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:38.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.898][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:38.899][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:38.900][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.901][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:38.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:38.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.909][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:38.910][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:38.911][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.912][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.913][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:38.914][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:38.915][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.916][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.917][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:38.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:38.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.924][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.925][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.926][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.926][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.934][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:38.935][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:38.936][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.937][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:38.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:38.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.952][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:38.953][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:38.954][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.955][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.956][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:38.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:38.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.962][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:38.963][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:38.964][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.965][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.966][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:38.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:38.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:38.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:38.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:38.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:38.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:38.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:38.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:38.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:38.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:38.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:38.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:38.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:38.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:38.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:38.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:39.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:39.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:39.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:39.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:39.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:39.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:39.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:39.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:39.009][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2022-10-18 18:47:39.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:39.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:39.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:39.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:39.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:39.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:39.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:39.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:39.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:39.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:39.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:39.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:39.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:39.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:39.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:39.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:39.030][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2022-10-18 18:47:39.031][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:39.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2022-10-18 18:47:39.034][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:39.035][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:39.036][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:39.037][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:39.037][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:39.038][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:39.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:39.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:39.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:39.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:39.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:39.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:39.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:39.051][scheduler$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 18:47:39.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:39.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:39.055][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2022-10-18 18:47:39.478][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2022-10-18 18:47:39.907][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:39.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2022-10-18 18:47:39.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2022-10-18 18:47:39.936][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2022-10-18 18:47:39.941][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:39.956][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:39.957][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:39.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:39.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:39.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:39.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:39.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:39.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:39.969][FUN] Functions in observer BiodbConfig: [21]: ".__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 18:47:39.971][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:39.973][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:39.973][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.974][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:39.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:39.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:39.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:39.983][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:39.984][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:39.985][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.986][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:39.987][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:39.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:39.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:39.993][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:39.994][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:39.995][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:39.996][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:39.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:39.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:39.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.004][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:40.005][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:40.006][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.007][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:40.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:40.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.015][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:40.016][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:40.017][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.018][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:40.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:40.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.025][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:40.026][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:40.027][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.028][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.029][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:40.030][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:40.031][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.032][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.033][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:40.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.040][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:40.041][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:40.042][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.043][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:40.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:40.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.050][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:40.051][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:40.052][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.053][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.054][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:40.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:40.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.061][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:40.062][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:40.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.064][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.065][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:40.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:40.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.079][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:40.080][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:40.081][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.082][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.083][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:40.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:40.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:40.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:40.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:40.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:40.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:40.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:40.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:40.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:40.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:40.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:40.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:40.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:40.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:40.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:40.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:40.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:40.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:40.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:40.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:40.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:40.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:40.128][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2022-10-18 18:47:40.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:40.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:40.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:40.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:40.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:40.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:40.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:40.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:40.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:40.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:40.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:40.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:40.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:40.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:40.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:40.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:40.149][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2022-10-18 18:47:40.150][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:40.152][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2022-10-18 18:47:40.153][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:40.154][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:40.155][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:40.156][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:40.157][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:40.158][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:40.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:40.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:40.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:40.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:40.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:40.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:40.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:40.170][scheduler$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 18:47:40.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:40.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:40.175][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2022-10-18 18:47:40.584][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2022-10-18 18:47:41.019][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2022-10-18 18:47:41.024][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2022-10-18 18:47:41.028][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2022-10-18 18:47:41.039][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2022-10-18 18:47:41.049][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2022-10-18 18:47:41.053][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:41.069][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:41.070][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:41.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:41.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:41.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:41.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:41.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:41.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:41.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:41.084][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:41.085][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:41.085][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.086][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:41.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:41.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.094][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:41.095][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:41.096][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.097][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.098][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:41.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:41.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.105][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:41.106][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:41.107][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.108][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.109][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:41.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:41.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.116][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:41.117][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:41.118][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.119][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:41.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:41.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.127][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:41.128][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:41.129][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.130][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:41.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:41.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.138][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:41.139][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:41.140][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.141][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.142][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:41.143][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:41.144][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.145][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.146][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:41.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:41.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.154][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:41.155][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:41.156][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.157][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:41.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:41.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.165][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:41.166][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:41.167][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.168][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:41.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:41.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.177][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:41.178][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:41.179][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.180][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.181][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:41.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:41.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.188][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:41.189][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:41.190][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.191][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.202][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:41.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:41.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:41.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:41.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:41.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:41.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:41.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:41.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:41.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:41.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:41.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:41.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:41.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:41.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:41.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:41.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:41.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:41.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:41.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:41.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:41.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:41.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:41.248][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2022-10-18 18:47:41.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:41.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:41.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:41.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:41.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:41.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:41.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:41.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:41.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:41.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:41.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:41.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:41.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:41.269][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 18:47:41.270][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2022-10-18 18:47:41.271][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:41.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2022-10-18 18:47:41.274][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:41.275][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:41.276][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:41.277][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:41.278][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:41.278][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:41.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:41.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:41.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:41.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:41.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:41.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:41.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:41.292][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2022-10-18 18:47:41.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:41.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:41.296][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2022-10-18 18:47:41.710][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 18:47:42.134][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:42.141][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2022-10-18 18:47:42.152][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2022-10-18 18:47:42.162][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2022-10-18 18:47:42.166][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:42.181][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:42.183][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:42.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:42.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:42.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:42.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:42.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:42.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:42.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:42.200][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:42.201][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:42.202][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.203][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:42.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:42.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.211][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:42.212][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:42.213][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.214][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.215][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:42.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:42.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.222][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:42.223][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:42.224][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.225][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.227][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:42.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:42.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.234][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:42.235][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:42.236][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.236][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:42.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:42.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.244][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:42.245][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:42.246][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.247][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:42.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:42.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.256][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:42.257][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:42.258][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.259][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.260][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:42.261][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:42.262][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.263][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.264][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:42.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:42.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.271][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:42.272][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:42.273][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.274][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:42.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:42.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.282][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:42.283][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:42.284][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.285][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:42.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:42.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.293][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:42.294][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:42.295][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.296][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:42.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:42.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.303][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:42.304][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:42.305][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.306][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.307][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:42.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:42.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:42.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:42.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:42.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:42.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:42.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:42.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:42.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:42.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:42.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:42.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:42.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:42.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:42.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:42.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:42.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:42.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:42.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:42.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:42.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:42.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:42.360][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2022-10-18 18:47:42.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:42.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:42.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:42.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:42.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:42.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:42.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:42.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:42.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:42.402][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 18:47:42.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:42.406][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:42.408][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 18:47:42.937][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 18:47:43.505][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:43.516][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2022-10-18 18:47:43.533][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2022-10-18 18:47:43.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:43.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:43.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:43.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:43.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:43.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:43.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:43.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:43.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:43.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:43.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:43.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:44.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:44.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:44.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:44.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:44.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:44.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:44.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:44.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:44.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:44.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:44.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:44.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:44.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:44.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:44.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:44.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:44.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:44.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:44.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:44.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:44.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:44.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:44.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:44.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:44.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:44.154][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:44.157][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:44.158][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:44.160][private$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 18:47:44.610][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 18:47:45.128][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:45.135][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2022-10-18 18:47:45.146][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2022-10-18 18:47:45.152][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 18:47:45.155][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:45.156][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:45.158][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 18:47:45.579][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 18:47:46.012][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:46.020][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2022-10-18 18:47:46.033][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2022-10-18 18:47:46.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:46.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:46.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:46.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:46.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:46.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:46.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:46.050][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2022-10-18 18:47:46.051][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:46.052][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2022-10-18 18:47:46.054][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:46.055][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:46.056][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:46.057][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:46.058][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:46.059][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:46.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:46.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:46.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:46.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:46.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:46.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:46.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:46.072][scheduler$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 18:47:46.075][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:46.076][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:46.077][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2022-10-18 18:47:46.497][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2022-10-18 18:47:46.931][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:46.940][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2022-10-18 18:47:46.967][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2022-10-18 18:47:46.980][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2022-10-18 18:47:46.985][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:46.999][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:47.001][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:47.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:47.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:47.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:47.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:47.010][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 18:47:47.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:47.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:47.014][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:47.015][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:47.016][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.016][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:47.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:47.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.024][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:47.025][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:47.026][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.027][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.028][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:47.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:47.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.035][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:47.036][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:47.037][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.038][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.039][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:47.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:47.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.046][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:47.047][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:47.048][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.049][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:47.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:47.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.058][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:47.059][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:47.059][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.060][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:47.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:47.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.069][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:47.070][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:47.071][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.072][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.073][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:47.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:47.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.080][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:47.081][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:47.082][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.083][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.084][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:47.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:47.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.092][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.093][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.094][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.102][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:47.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:47.104][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.105][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:47.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:47.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.113][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:47.114][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:47.115][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.116][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.117][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:47.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:47.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.124][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:47.124][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:47.125][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.126][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.127][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:47.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:47.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:47.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:47.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:47.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:47.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:47.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:47.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:47.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:47.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:47.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:47.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:47.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:47.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:47.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:47.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:47.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:47.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:47.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:47.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:47.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:47.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:47.176][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2022-10-18 18:47:47.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:47.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:47.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:47.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:47.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:47.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:47.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:47.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:47.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:47.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:47.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:47.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:47.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:47.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:47.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:47.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:47.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:47.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:47.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:47.222][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2022-10-18 18:47:47.223][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:47.225][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2022-10-18 18:47:47.227][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:47.228][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:47.229][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:47.230][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:47.231][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:47.231][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:47.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:47.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:47.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:47.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:47.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:47.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:47.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:47.245][scheduler$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 18:47:47.248][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:47.249][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:47.256][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2022-10-18 18:47:47.678][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2022-10-18 18:47:48.142][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:48.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2022-10-18 18:47:48.161][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2022-10-18 18:47:48.172][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2022-10-18 18:47:48.176][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:48.191][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:48.192][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:48.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.207][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:48.208][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:48.209][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.210][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:48.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:48.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.218][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:48.219][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:48.220][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.221][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.223][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:48.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:48.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.230][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:48.231][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:48.232][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.233][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:48.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:48.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.241][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:48.242][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:48.243][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.244][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:48.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:48.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.252][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:48.254][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:48.255][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.255][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:48.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:48.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.264][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:48.265][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:48.266][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.267][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.268][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:48.270][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:48.271][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.272][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.273][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:48.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:48.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.280][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.281][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.282][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.283][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.292][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:48.293][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:48.294][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.295][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:48.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:48.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.304][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:48.305][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:48.306][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.307][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.309][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:48.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:48.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.316][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:48.317][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:48.318][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.319][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.321][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:48.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:48.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:48.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:48.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:48.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:48.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:48.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:48.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:48.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:48.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:48.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:48.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:48.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:48.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:48.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:48.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:48.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:48.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:48.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:48.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:48.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:48.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.373][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2022-10-18 18:47:48.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.431][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:48.435][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:48.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 18:47:48.438][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:48.439][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-10-18 18:47:48.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:48.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:48.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:48.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:48.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:48.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:48.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:48.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:48.961][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:48.964][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:48.966][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-10-18 18:47:48.968][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:48.969][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-10-18 18:47:48.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:48.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:48.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:48.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:49.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:49.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.455][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:49.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:49.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:49.475][biodb::testThat]
biodb.INFO [2022-10-18 18:47:49.476][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-10-18 18:47:49.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:49.478][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:49.481][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:49.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:49.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:49.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:49.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:49.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:49.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:49.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:49.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:49.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:49.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:49.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:49.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:49.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:49.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:49.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:49.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:49.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:49.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:49.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:49.562][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:49.566][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:49.567][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:49.569][private$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 18:47:49.986][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 18:47:50.417][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:50.425][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2022-10-18 18:47:50.438][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2022-10-18 18:47:50.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:50.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:50.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:50.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:50.453][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 18:47:50.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:50.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:50.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:50.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:50.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:50.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:50.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:50.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:50.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:50.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:50.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:50.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:50.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:50.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:50.468][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 18:47:50.471][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:50.472][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:50.474][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 18:47:50.885][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 18:47:51.317][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:51.324][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2022-10-18 18:47:51.336][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2022-10-18 18:47:51.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:51.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:51.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:51.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:51.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:51.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:51.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:51.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:51.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:51.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:51.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:51.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:51.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:51.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:51.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:51.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:51.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:51.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:51.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:51.364][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:51.367][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:51.368][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:51.370][private$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 18:47:51.780][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 18:47:52.228][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:52.235][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2022-10-18 18:47:52.247][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2022-10-18 18:47:52.253][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:47:52.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:52.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:52.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:52.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:52.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:52.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:52.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:52.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.274][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:52.275][private$selectFields]
biodb.TRACE[2022-10-18 18:47:52.275][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:52.276][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:52.277][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:52.278][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.279][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.280][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.281][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.282][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.283][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.284][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.285][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.285][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:52.286][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:52.287][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.288][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.289][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.290][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.291][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:52.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.312][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2022-10-18 18:47:52.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:52.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:52.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:52.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:52.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:52.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:52.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:52.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.331][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:52.332][private$selectFields]
biodb.TRACE[2022-10-18 18:47:52.332][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:52.333][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:52.334][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:52.335][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.336][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.337][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.338][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.339][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.341][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.342][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.343][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:52.343][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:52.344][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.345][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.346][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.347][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.348][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:52.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:52.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.361][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 18:47:52.361][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:47:52.362][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 18:47:52.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:52.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:52.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:52.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:52.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:52.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:52.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:52.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:52.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:52.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:52.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:52.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:52.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:52.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:52.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:52.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:52.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:52.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:52.508][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:52.512][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:52.513][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:52.515][private$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 18:47:52.967][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 18:47:53.442][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:53.451][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2022-10-18 18:47:53.463][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2022-10-18 18:47:53.470][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 18:47:53.474][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:53.475][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:53.477][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-10-18 18:47:53.891][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-10-18 18:47:54.340][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:54.353][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2022-10-18 18:47:54.376][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2022-10-18 18:47:54.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:54.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:54.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:54.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:54.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:54.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:54.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:54.514][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:47:54.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:54.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.566][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.567][private$selectFields]
biodb.TRACE[2022-10-18 18:47:54.568][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:54.569][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:54.570][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.571][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.572][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.573][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.574][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.575][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.576][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.577][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.578][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.579][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.580][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.581][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.582][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.583][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.584][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.586][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:54.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.620][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-10-18 18:47:54.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.635][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 18:47:54.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.636][FUN] Functions in observer BiodbConfig: [21]: ".__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 18:47:54.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.679][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.681][private$selectFields]
biodb.TRACE[2022-10-18 18:47:54.682][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:54.683][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:54.684][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.687][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.688][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.689][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.690][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.691][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.692][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.693][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.704][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.705][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.706][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.707][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.708][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.709][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:54.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.723][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 18:47:54.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:54.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.747][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.748][private$selectFields]
biodb.TRACE[2022-10-18 18:47:54.749][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:54.750][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:54.751][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.752][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.754][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.755][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.756][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.757][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.758][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.759][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.760][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.761][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.762][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:54.763][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.764][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.765][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.766][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.767][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:54.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:54.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.781][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-10-18 18:47:54.783][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:47:54.784][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 18:47:54.792][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:54.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:54.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:54.798][biodb::testThat]
biodb.INFO [2022-10-18 18:47:54.799][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-10-18 18:47:54.800][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:54.801][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:54.805][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:54.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:54.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:54.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:54.894][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:54.898][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:54.900][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2022-10-18 18:47:54.902][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:54.903][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2022-10-18 18:47:54.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:54.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:54.934][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:54.937][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:54.939][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2022-10-18 18:47:54.940][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:54.942][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2022-10-18 18:47:54.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:54.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:54.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:54.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:54.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:54.978][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:54.982][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:54.983][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2022-10-18 18:47:54.984][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:54.986][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2022-10-18 18:47:54.988][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:47:54.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.009][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.010][private$selectFields]
biodb.TRACE[2022-10-18 18:47:55.011][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:55.012][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:55.013][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.015][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.016][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.017][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.019][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.020][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.020][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.021][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.022][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.023][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.024][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.025][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.026][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.027][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:55.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.040][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2022-10-18 18:47:55.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.050][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 18:47:55.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.059][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.060][private$selectFields]
biodb.TRACE[2022-10-18 18:47:55.061][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:55.062][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:55.063][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.064][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.065][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.066][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.067][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.068][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.069][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.069][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.070][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.071][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.072][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.073][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.074][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.075][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.076][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.077][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:55.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.090][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 18:47:55.091][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:47:55.092][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 18:47:55.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:55.178][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 18:47:55.181][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:55.182][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2022-10-18 18:47:55.184][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:55.185][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2022-10-18 18:47:55.188][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 18:47:55.191][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:55.192][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2022-10-18 18:47:55.193][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:55.195][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2022-10-18 18:47:55.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.229][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.TRACE[2022-10-18 18:47:55.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.266][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:47:55.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.275][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 18:47:55.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.286][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.287][private$selectFields]
biodb.TRACE[2022-10-18 18:47:55.288][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:55.289][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:55.290][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.291][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.292][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.293][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.294][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.295][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.296][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.297][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.298][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.299][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.305][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.306][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.308][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.309][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.310][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.311][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:55.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.324][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-10-18 18:47:55.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.344][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.345][private$selectFields]
biodb.TRACE[2022-10-18 18:47:55.345][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:55.346][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:55.347][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.348][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.349][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.350][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.351][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.352][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.353][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.354][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.355][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.356][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.357][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.358][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.359][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.360][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.361][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.362][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.375][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 18:47:55.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.396][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.397][private$selectFields]
biodb.TRACE[2022-10-18 18:47:55.398][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:55.399][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:55.400][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.403][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.404][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.405][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.406][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.407][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.408][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.409][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.410][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.411][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.412][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.413][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.413][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.414][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.415][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:55.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.429][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-10-18 18:47:55.430][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:47:55.431][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 18:47:55.439][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:55.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:55.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:55.445][biodb::testThat]
biodb.INFO [2022-10-18 18:47:55.446][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-10-18 18:47:55.447][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:55.448][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:55.451][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:55.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:55.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:55.530][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 18:47:55.533][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:55.535][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2022-10-18 18:47:55.536][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:55.537][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2022-10-18 18:47:55.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.563][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 18:47:55.566][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:55.567][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2022-10-18 18:47:55.568][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:55.570][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2022-10-18 18:47:55.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.580][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 18:47:55.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.581][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 18:47:55.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:55.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.595][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 18:47:55.598][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:55.599][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2022-10-18 18:47:55.600][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:55.601][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2022-10-18 18:47:55.604][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:47:55.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.614][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 18:47:55.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.624][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.625][private$selectFields]
biodb.TRACE[2022-10-18 18:47:55.626][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:55.627][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:55.628][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.634][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.636][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.637][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.638][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.639][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.640][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.641][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.642][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.643][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.644][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.645][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.646][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.646][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.647][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.648][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:55.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.661][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2022-10-18 18:47:55.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.680][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.681][private$selectFields]
biodb.TRACE[2022-10-18 18:47:55.682][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:55.683][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:55.684][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.687][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.688][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.689][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.690][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.691][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.691][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.692][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.693][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.694][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.695][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.696][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.697][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.698][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:55.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.711][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 18:47:55.712][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:47:55.713][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 18:47:55.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:55.808][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:55.812][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:55.813][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2022-10-18 18:47:55.815][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:55.816][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2022-10-18 18:47:55.819][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:47:55.822][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:55.823][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2022-10-18 18:47:55.824][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:55.826][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2022-10-18 18:47:55.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:55.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:55.898][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:47:55.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.918][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.919][private$selectFields]
biodb.TRACE[2022-10-18 18:47:55.919][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:55.920][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:55.921][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.922][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.923][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.924][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.925][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.926][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.927][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.928][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.929][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.930][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.931][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.932][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.933][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.934][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.935][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.936][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:55.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.949][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-10-18 18:47:55.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:55.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:55.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:55.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:55.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:55.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:55.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:55.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.975][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.976][private$selectFields]
biodb.TRACE[2022-10-18 18:47:55.976][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:55.977][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:55.978][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.979][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.981][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.982][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.983][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.984][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.985][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.985][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.986][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.987][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:55.988][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.989][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.990][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.991][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.992][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:55.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:55.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:55.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:55.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.004][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-10-18 18:47:56.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:56.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:56.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:56.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:56.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:56.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:56.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:56.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.024][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:56.025][private$selectFields]
biodb.TRACE[2022-10-18 18:47:56.026][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:56.026][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:56.027][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:56.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.029][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.030][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.031][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.032][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.033][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.034][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.035][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.036][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:56.037][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-10-18 18:47:56.037][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.038][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.039][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.040][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.041][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-10-18 18:47:56.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:56.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:56.054][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-10-18 18:47:56.055][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:47:56.056][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 18:47:56.075][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:56.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:56.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:56.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:56.080][biodb::testThat]
biodb.INFO [2022-10-18 18:47:56.081][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2022-10-18 18:47:56.082][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:56.083][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:56.085][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-10-18 18:47:56.086][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:56.088][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-10-18 18:47:56.090][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:47:56.091][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:56.092][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:56.093][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:56.094][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:56.095][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:56.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:56.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:56.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:56.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:56.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:56.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:56.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:56.110][scheduler$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 18:47:56.112][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:56.113][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:56.115][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2022-10-18 18:47:56.549][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2022-10-18 18:47:56.975][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:56.982][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2022-10-18 18:47:56.993][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2022-10-18 18:47:57.003][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2022-10-18 18:47:57.007][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:57.023][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:57.024][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:47:57.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:57.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:57.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:57.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:57.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:57.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:57.036][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.TRACE[2022-10-18 18:47:57.038][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.039][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.040][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.041][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.049][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:47:57.051][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:47:57.052][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.053][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.054][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:57.055][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:57.056][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.057][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.058][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:47:57.059][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:47:57.060][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.061][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.062][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:47:57.063][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:47:57.064][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.065][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.066][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:57.067][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:57.068][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.069][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.070][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:47:57.071][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:57.072][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.072][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.074][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:57.075][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:57.075][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.076][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.078][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:57.079][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.079][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.080][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.082][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:47:57.083][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:47:57.084][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.085][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.086][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:47:57.096][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:47:57.097][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.098][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:57.150][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2022-10-18 18:47:57.151][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2022-10-18 18:47:57.158][biodb::testThat]
biodb.INFO [2022-10-18 18:47:57.159][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 18:47:57.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:57.161][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:57.172][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2022-10-18 18:47:57.173][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2022-10-18 18:47:57.174][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2022-10-18 18:47:57.176][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2022-10-18 18:47:57.177][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2022-10-18 18:47:57.178][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:57.179][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:57.181][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:47:57.182][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:57.183][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:57.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:57.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:57.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:57.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:57.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:57.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:57.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:57.198][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2022-10-18 18:47:57.201][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:57.202][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:57.203][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2022-10-18 18:47:57.624][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 18:47:58.071][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:58.084][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2022-10-18 18:47:58.104][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2022-10-18 18:47:58.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:58.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:58.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:58.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:58.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:58.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:58.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:58.131][scheduler$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 18:47:58.135][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:58.137][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:58.139][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2022-10-18 18:47:58.567][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2022-10-18 18:47:59.027][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:59.034][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2022-10-18 18:47:59.045][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2022-10-18 18:47:59.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:59.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:59.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:59.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:59.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:59.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:59.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:59.060][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2022-10-18 18:47:59.063][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:59.063][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:59.065][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2022-10-18 18:48:00.198][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 18:48:00.700][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:00.712][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2022-10-18 18:48:00.757][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2022-10-18 18:48:00.774][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2022-10-18 18:48:00.779][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:48:00.794][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2022-10-18 18:48:00.795][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2022-10-18 18:48:00.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:00.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:00.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:00.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:00.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:00.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:00.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:00.809][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:00.810][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:00.811][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.812][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:00.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:00.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.820][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:48:00.821][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:48:00.822][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.823][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.824][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:48:00.825][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:48:00.826][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.827][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.828][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:48:00.829][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:48:00.830][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.831][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.832][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:48:00.833][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:48:00.834][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.835][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.836][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:00.837][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:00.838][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.839][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.841][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:48:00.842][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:48:00.843][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.844][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.845][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:00.846][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:00.847][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.848][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.849][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:00.850][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:00.851][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.852][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.853][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:48:00.854][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:48:00.855][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.856][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.857][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:48:00.858][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:48:00.859][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.860][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:00.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:00.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:00.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:00.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:00.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:00.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:00.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:00.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:00.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:00.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:00.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:00.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:00.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:00.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:48:00.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:00.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:00.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:00.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:00.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:00.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:00.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:00.902][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:00.903][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:00.904][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.905][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:00.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.913][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:48:00.914][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:48:00.915][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.916][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.917][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:48:00.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:48:00.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.923][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:48:00.925][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:48:00.925][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.926][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.928][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:48:00.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:48:00.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.934][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:48:00.935][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:48:00.936][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.937][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:48:00.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:48:00.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.945][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:48:00.946][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:48:00.947][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.948][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:48:00.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:48:00.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.956][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:00.957][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:00.958][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.959][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.960][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:00.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:00.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.967][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:48:00.968][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:48:00.969][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.970][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.971][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:48:00.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:48:00.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.978][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:00.979][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:00.980][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.981][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:00.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:00.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.989][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:00.990][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:00.991][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.992][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:00.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:00.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:00.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:00.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.001][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:48:01.002][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:48:01.003][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.004][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.005][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:48:01.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:48:01.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.012][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:48:01.013][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:48:01.014][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.015][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.016][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:48:01.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:48:01.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:48:01.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:01.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:01.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:01.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:01.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:01.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:01.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:01.064][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.065][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.066][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.067][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.075][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:48:01.076][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:48:01.077][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.078][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.079][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:48:01.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:48:01.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.094][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:48:01.095][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:48:01.096][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.097][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:48:01.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:48:01.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.105][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:48:01.107][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:48:01.108][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.108][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:48:01.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:48:01.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.117][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:48:01.118][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:48:01.119][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.120][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:48:01.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:48:01.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.128][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:01.129][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:01.130][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.131][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.132][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:01.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:01.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.139][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:48:01.140][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:48:01.141][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.142][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.143][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:48:01.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:48:01.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.150][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:01.151][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:01.152][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.152][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:01.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:01.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.160][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:01.161][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:01.162][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.163][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:01.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:01.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.171][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:48:01.172][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:48:01.173][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.174][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.175][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:48:01.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:48:01.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.183][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:48:01.184][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:48:01.185][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.186][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.187][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:48:01.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:48:01.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:01.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:01.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:01.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:01.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:01.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:48:01.260][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2022-10-18 18:48:01.261][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2022-10-18 18:48:01.262][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-10-18 18:48:01.273][biodb::testThat]
biodb.INFO [2022-10-18 18:48:01.274][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2022-10-18 18:48:01.275][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:01.276][biodb::testThat]
biodb.INFO [2022-10-18 18:48:01.297][biodb::testThat]
biodb.INFO [2022-10-18 18:48:01.299][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2022-10-18 18:48:01.300][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:01.301][biodb::testThat]
biodb.INFO [2022-10-18 18:48:01.307][biodb::testThat]
biodb.INFO [2022-10-18 18:48:01.308][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2022-10-18 18:48:01.309][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:01.309][biodb::testThat]
biodb.DEBUG[2022-10-18 18:48:01.312][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:48:01.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:01.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:01.318][private$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 18:48:01.810][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 18:48:02.442][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:02.449][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2022-10-18 18:48:02.460][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2022-10-18 18:48:02.476][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:02.477][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:02.478][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:02.479][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:02.480][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:02.482][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:02.483][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:02.484][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:48:02.494][biodb::testThat]
biodb.INFO [2022-10-18 18:48:02.496][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2022-10-18 18:48:02.497][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:02.498][biodb::testThat]
biodb.ERROR[2022-10-18 18:48:02.511][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-10-18 18:48:02.526][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-10-18 18:48:02.539][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:48:02.541][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-10-18 18:48:02.542][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-10-18 18:48:02.544][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:48:02.545][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:02.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:02.547][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.549][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 18:48:02.559][biodb::testContext]
biodb.INFO [2022-10-18 18:48:02.560][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:48:02.561][biodb::testContext] Test context - Test conversions
biodb.INFO [2022-10-18 18:48:02.562][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:48:02.563][biodb::testContext]
biodb.INFO [2022-10-18 18:48:02.568][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:48:02.570][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:48:02.574][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:48:02.575][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:48:02.576][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:48:02.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.579][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:48:02.580][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:48:02.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.583][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.DEBUG[2022-10-18 18:48:02.584][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:48:02.585][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:48:02.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.588][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:48:02.589][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:48:02.590][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:48:02.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.592][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 18:48:02.593][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:48:02.594][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:48:02.595][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:48:02.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.599][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:48:02.600][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:48:02.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.603][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:48:02.604][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:48:02.605][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:48:02.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.609][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:48:02.610][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:48:02.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.614][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:48:02.615][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:48:02.616][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:48:02.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.620][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:48:02.621][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:48:02.622][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:48:02.623][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:48:02.624][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:48:02.625][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:48:02.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.629][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:48:02.630][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:48:02.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.634][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:48:02.635][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:48:02.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.639][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:48:02.640][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:48:02.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.644][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:48:02.645][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:48:02.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.648][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 18:48:02.649][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:48:02.650][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:48:02.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.653][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:48:02.654][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:48:02.658][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:48:02.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.661][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:48:02.662][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:48:02.663][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:48:02.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.667][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:48:02.669][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.670][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 18:48:02.671][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.672][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:02.673][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.674][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.675][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.676][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.677][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:48:02.678][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:02.679][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.680][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:48:02.681][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:02.682][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.683][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.684][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:48:02.684][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:48:02.684][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:48:02.684][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:48:02.684][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:48:02.685][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:02.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:02.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:02.687][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:02.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:02.689][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:02.690][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.691][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:02.692][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:02.693][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.694][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.695][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:48:02.697][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.698][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:48:02.699][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:02.700][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.701][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.702][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.703][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.704][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:48:02.705][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:02.706][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.707][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:48:02.708][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:02.709][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.710][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.711][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:48:02.711][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:48:02.711][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:48:02.711][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:48:02.711][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:48:02.712][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:02.712][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:02.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:02.714][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:02.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:02.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:02.717][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.718][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.719][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:02.719][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:02.720][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.721][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.722][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:48:02.724][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.725][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 18:48:02.726][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.727][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:02.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.728][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.729][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.730][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.731][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:48:02.732][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:02.733][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.734][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:48:02.735][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:02.736][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.736][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.737][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.738][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:02.739][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:02.740][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:02.741][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:02.742][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:02.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:02.743][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.744][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.745][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:02.746][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:02.747][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.748][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.749][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:48:02.751][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.752][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:48:02.753][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.754][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:02.755][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.756][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.757][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.758][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.759][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:48:02.760][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:02.761][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.761][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:48:02.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:02.763][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.764][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:02.765][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.766][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:02.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:02.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:02.769][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:02.770][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:02.771][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:02.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:02.773][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.774][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:02.775][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:02.776][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:02.777][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:02.778][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:48:02.779][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.792][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 18:48:02.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.801][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 18:48:02.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.803][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 18:48:02.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.805][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 18:48:02.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.821][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 18:48:02.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.827][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 18:48:02.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.844][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 18:48:02.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.846][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 18:48:02.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.850][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 18:48:02.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.859][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 18:48:02.860][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:48:02.861][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:48:02.863][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:48:02.864][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:48:02.865][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:48:02.866][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:48:02.868][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:48:02.869][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:48:02.870][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:48:02.871][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:48:02.873][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:48:02.874][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:48:02.875][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:48:02.876][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:48:02.877][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:48:02.879][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:48:02.880][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:48:02.881][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:48:02.882][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:48:02.884][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:48:02.885][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:48:02.886][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:48:02.887][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:48:02.889][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:48:02.890][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:48:02.891][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:48:02.892][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:48:02.893][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:48:02.895][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:48:02.896][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:48:02.897][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:48:02.899][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:48:02.900][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:48:02.901][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:48:02.902][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:48:02.904][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:48:02.905][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:48:02.906][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:48:02.908][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:48:02.909][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:48:02.910][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:48:02.912][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:48:02.913][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:48:02.914][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:48:02.916][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:48:02.917][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:48:02.918][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:48:02.920][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:48:02.921][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:48:02.922][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:48:02.924][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:48:02.925][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:48:02.926][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:48:02.928][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:48:02.929][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:48:02.930][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:48:02.932][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:48:02.933][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:48:02.934][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:48:02.935][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:48:02.937][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:48:02.938][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:48:02.939][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:48:02.941][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:48:02.942][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:48:02.943][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:48:02.945][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:48:02.946][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:48:02.947][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:48:02.949][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:48:02.950][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:48:02.952][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:48:02.953][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:48:02.954][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:48:02.956][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:48:02.957][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:48:02.958][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:48:02.960][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:48:02.961][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:48:02.962][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:48:02.964][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:48:02.965][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:48:02.967][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:48:02.968][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:48:02.970][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:48:02.971][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:48:02.972][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.974][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:02.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:02.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:02.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:02.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:02.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:02.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:02.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.993][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 18:48:02.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:02.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:02.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:02.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:02.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:02.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:02.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.004][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 18:48:03.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.010][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 18:48:03.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.016][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 18:48:03.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:03.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.024][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 18:48:03.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:03.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:03.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.036][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 18:48:03.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:03.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.047][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 18:48:03.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.048][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.DEBUG[2022-10-18 18:48:03.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.053][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 18:48:03.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:03.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.065][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 18:48:03.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:03.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:03.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:03.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:03.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:03.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:03.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:03.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:03.080][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-10-18 18:48:03.082][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-10-18 18:48:03.084][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:03.085][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:48:03.086][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:03.087][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:03.088][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:03.089][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:03.090][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:03.091][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-10-18 18:48:03.092][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 18:48:03.093][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:03.094][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:03.095][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-10-18 18:48:03.096][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-10-18 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-10-18 18:48:03.097][self$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 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-10-18 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-10-18 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-10-18 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-10-18 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-10-18 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-10-18 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-10-18 18:48:03.097][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-10-18 18:48:03.098][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:03.099][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:48:03.099][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:48:03.099][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:48:03.100][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 18:48:03.101][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:03.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:03.103][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:03.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:03.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:03.105][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:03.106][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:48:03.106][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-10-18 18:48:03.107][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:03.108][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:03.109][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:03.117][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-10-18 18:48:03.117][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-10-18 18:48:03.119][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:48:03.121][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:48:03.123][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-10-18 18:48:03.124][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:48:03.126][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:48:03.127][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:48:03.131][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-10-18 18:48:03.132][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-10-18 18:48:03.133][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-10-18 18:48:03.135][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-10-18 18:48:03.136][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:48:03.137][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:48:03.138][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-10-18 18:48:03.140][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-10-18 18:48:03.141][biodb::testThat]
biodb.INFO [2022-10-18 18:48:03.142][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2022-10-18 18:48:03.143][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:03.144][biodb::testThat]
biodb.DEBUG[2022-10-18 18:48:03.148][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 18:48:03.152][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:03.153][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:03.155][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2022-10-18 18:48:03.559][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2022-10-18 18:48:04.606][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:04.620][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2022-10-18 18:48:04.651][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2022-10-18 18:48:04.661][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:48:04.665][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:04.666][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:04.668][private$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 18:48:05.086][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 18:48:05.517][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:05.526][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2022-10-18 18:48:05.541][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2022-10-18 18:48:05.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:05.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:05.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:05.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:05.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:05.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:05.558][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 18:48:05.560][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 18:48:05.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:05.565][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:05.567][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-10-18 18:48:06.732][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-10-18 18:48:07.191][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:07.202][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2022-10-18 18:48:07.219][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2022-10-18 18:48:07.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:07.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:07.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:07.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:07.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:07.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:07.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:07.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:07.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:07.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:07.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:07.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:07.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:07.281][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 18:48:07.307][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:48:07.313][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:48:07.315][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2022-10-18 18:48:07.317][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:48:07.319][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2022-10-18 18:48:07.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:07.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:07.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:07.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:07.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:07.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:07.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:07.339][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:48:07.344][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:48:07.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2022-10-18 18:48:07.348][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:48:07.350][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2022-10-18 18:48:07.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:07.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:07.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:07.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:07.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:07.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:07.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:07.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:07.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:07.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:07.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:07.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:07.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:07.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:07.388][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:48:07.392][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:48:07.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2022-10-18 18:48:07.396][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:48:07.398][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2022-10-18 18:48:07.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:07.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:07.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:07.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:07.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:07.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:07.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:07.418][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:48:07.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:48:07.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2022-10-18 18:48:07.426][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:48:07.428][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2022-10-18 18:48:07.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:07.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:07.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:07.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:07.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:07.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:07.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:07.448][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:48:07.453][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:07.454][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:07.457][private$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 18:48:07.882][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 18:48:08.312][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:08.319][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2022-10-18 18:48:08.331][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2022-10-18 18:48:08.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:08.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:08.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:08.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:08.353][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 18:48:08.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:08.355][FUN] Functions in observer BiodbConfig: [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 18:48:08.359][biodb::testThat]
biodb.INFO [2022-10-18 18:48:08.360][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2022-10-18 18:48:08.362][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:08.363][biodb::testThat]
biodb.DEBUG[2022-10-18 18:48:08.367][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 18:48:08.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:08.373][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:08.375][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-10-18 18:48:08.795][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-10-18 18:48:09.230][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:09.242][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2022-10-18 18:48:09.262][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2022-10-18 18:48:09.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:09.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:09.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:09.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:09.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:09.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:09.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:09.291][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:48:09.297][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:09.298][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:09.301][private$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 18:48:09.728][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 18:48:10.211][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:10.224][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2022-10-18 18:48:10.246][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2022-10-18 18:48:10.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:10.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.269][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 18:48:10.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.272][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.INFO [2022-10-18 18:48:10.276][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:48:10.278][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-10-18 18:48:10.280][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-10-18 18:48:10.281][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:48:10.283][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.285][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.288][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 18:48:10.299][biodb::testContext]
biodb.INFO [2022-10-18 18:48:10.302][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:48:10.305][biodb::testContext] Test context - Test web services
biodb.INFO [2022-10-18 18:48:10.307][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:48:10.308][biodb::testContext]
biodb.INFO [2022-10-18 18:48:10.313][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:48:10.315][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:48:10.319][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:48:10.320][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:48:10.321][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:48:10.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.325][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:48:10.326][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:48:10.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.330][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:48:10.331][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:48:10.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.335][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:48:10.336][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:48:10.337][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:48:10.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.341][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:48:10.342][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:48:10.343][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:48:10.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.347][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:48:10.348][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:48:10.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.352][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:48:10.353][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:48:10.354][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:48:10.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.358][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:48:10.359][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:48:10.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.364][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:48:10.365][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:48:10.366][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:48:10.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.370][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:48:10.371][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:48:10.372][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:48:10.373][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:48:10.374][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:48:10.375][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:48:10.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.379][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:48:10.380][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:48:10.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.384][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:48:10.385][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:48:10.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.388][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 18:48:10.389][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:48:10.390][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:48:10.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.394][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:48:10.395][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:48:10.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.398][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 18:48:10.399][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:48:10.400][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:48:10.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.404][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:48:10.405][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:48:10.411][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:48:10.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.414][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 18:48:10.415][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:48:10.416][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:48:10.417][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:48:10.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.421][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:48:10.423][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.424][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 18:48:10.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.426][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:10.427][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.428][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.429][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.430][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.431][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:48:10.432][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:10.433][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.434][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:48:10.435][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:10.436][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.437][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.438][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:48:10.438][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:48:10.438][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:48:10.438][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:48:10.438][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:48:10.439][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:10.440][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.441][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.442][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:10.443][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.445][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.446][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.447][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:10.447][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:10.448][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.449][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.451][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:48:10.452][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.453][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:48:10.454][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.455][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:10.456][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.457][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.458][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.459][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.460][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:48:10.461][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:10.462][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.463][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:48:10.464][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:10.465][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.466][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.467][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:48:10.467][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:48:10.467][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:48:10.467][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:48:10.467][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:48:10.468][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:10.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.471][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:10.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.474][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.475][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:10.476][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:10.477][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.478][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.479][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:48:10.481][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.482][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 18:48:10.483][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.484][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:10.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.487][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.489][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:48:10.490][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:10.491][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.492][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:48:10.493][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:10.494][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.495][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.496][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.497][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:10.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.499][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:10.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.503][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:10.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:10.506][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.507][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.508][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:48:10.509][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.510][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:48:10.511][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.512][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:10.513][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.514][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.515][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.516][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.517][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:48:10.518][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:10.519][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.520][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:48:10.521][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:10.522][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.523][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.524][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.525][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:10.526][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.527][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:10.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.530][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.531][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.532][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:10.533][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:10.534][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.535][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:10.536][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:48:10.537][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.545][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 18:48:10.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.547][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 18:48:10.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.549][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 18:48:10.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.551][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 18:48:10.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.558][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 18:48:10.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.560][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 18:48:10.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.578][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 18:48:10.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.583][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 18:48:10.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.584][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 18:48:10.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.591][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 18:48:10.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.604][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 18:48:10.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.610][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 18:48:10.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.615][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 18:48:10.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.620][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:48:10.622][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:48:10.623][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:48:10.624][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:48:10.626][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:48:10.627][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:48:10.629][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:48:10.630][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:48:10.631][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:48:10.633][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:48:10.634][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:48:10.635][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:48:10.637][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:48:10.638][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:48:10.639][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:48:10.641][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:48:10.642][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:48:10.643][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:48:10.645][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:48:10.646][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:48:10.648][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:48:10.649][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:48:10.650][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:48:10.652][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:48:10.653][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:48:10.654][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:48:10.656][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:48:10.657][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:48:10.658][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:48:10.660][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:48:10.661][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:48:10.662][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:48:10.664][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:48:10.665][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:48:10.666][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:48:10.668][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:48:10.669][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:48:10.670][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:48:10.672][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:48:10.673][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:48:10.674][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:48:10.676][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:48:10.677][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:48:10.679][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:48:10.680][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:48:10.681][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:48:10.683][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:48:10.684][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:48:10.686][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:48:10.687][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:48:10.688][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:48:10.690][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:48:10.691][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:48:10.692][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:48:10.694][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:48:10.695][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:48:10.696][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:48:10.698][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:48:10.699][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:48:10.701][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:48:10.702][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:48:10.703][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:48:10.705][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:48:10.706][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:48:10.708][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:48:10.709][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:48:10.711][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:48:10.712][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:48:10.713][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:48:10.715][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:48:10.716][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:48:10.718][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:48:10.719][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:48:10.721][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:48:10.722][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:48:10.723][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:48:10.725][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:48:10.726][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:48:10.728][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:48:10.729][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:48:10.730][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:48:10.732][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:48:10.733][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:48:10.735][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:48:10.736][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:48:10.737][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:48:10.738][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.740][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.746][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 18:48:10.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.787][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 18:48:10.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.821][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 18:48:10.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.825][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 18:48:10.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.840][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 18:48:10.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:10.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:10.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:10.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:10.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:10.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:10.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:10.855][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-10-18 18:48:10.857][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-10-18 18:48:10.859][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.860][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.861][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.862][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:10.863][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.864][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.865][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.866][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-10-18 18:48:10.868][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 18:48:10.869][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:10.870][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.871][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-10-18 18:48:10.872][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-10-18 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-10-18 18:48:10.873][self$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 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-10-18 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-10-18 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-10-18 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-10-18 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-10-18 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-10-18 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-10-18 18:48:10.873][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-10-18 18:48:10.874][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:10.875][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:48:10.875][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:48:10.875][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:48:10.877][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 18:48:10.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.880][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:10.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:10.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:10.883][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:10.884][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:48:10.884][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-10-18 18:48:10.885][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:10.886][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:10.895][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:10.897][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-10-18 18:48:10.897][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-10-18 18:48:10.899][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:48:10.901][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:48:10.903][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-10-18 18:48:10.904][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:48:10.906][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:48:10.907][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:48:10.911][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-10-18 18:48:10.912][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-10-18 18:48:10.913][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-10-18 18:48:10.915][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-10-18 18:48:10.916][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:48:10.917][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:48:10.919][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-10-18 18:48:10.920][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-10-18 18:48:10.921][biodb::testThat]
biodb.INFO [2022-10-18 18:48:10.922][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2022-10-18 18:48:10.923][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:10.924][biodb::testThat]
biodb.DEBUG[2022-10-18 18:48:10.928][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 18:48:10.932][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:48:10.934][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-10-18 18:48:10.935][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:48:10.937][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-10-18 18:48:10.941][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 18:48:10.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:10.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:10.948][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-10-18 18:48:11.385][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-10-18 18:48:11.815][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:11.823][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2022-10-18 18:48:11.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2022-10-18 18:48:11.843][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:48:11.844][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-10-18 18:48:11.845][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-10-18 18:48:11.846][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:48:11.847][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:11.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:11.849][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:11.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:11.851][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 18:48:11.856][biodb::testContext]
biodb.INFO [2022-10-18 18:48:11.857][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:48:11.858][biodb::testContext] Test context - Non regression tests
biodb.INFO [2022-10-18 18:48:11.859][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:48:11.860][biodb::testContext]
biodb.INFO [2022-10-18 18:48:11.866][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:48:11.867][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:48:11.872][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:48:11.873][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:48:11.874][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:48:11.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.877][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 18:48:11.878][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:48:11.879][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:48:11.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.883][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:48:11.884][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:48:11.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.887][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 18:48:11.888][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:48:11.889][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:48:11.890][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:48:11.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.894][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:48:11.895][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:48:11.896][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:48:11.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.900][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:48:11.901][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:48:11.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.904][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:48:11.905][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:48:11.907][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:48:11.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.910][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:48:11.911][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:48:11.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.915][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:48:11.916][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:48:11.917][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:48:11.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.921][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:48:11.922][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:48:11.923][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:48:11.924][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:48:11.925][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:48:11.926][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:48:11.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.930][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:48:11.931][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:48:11.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.935][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:48:11.936][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:48:11.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.940][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:48:11.941][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:48:11.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.945][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:48:11.946][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:48:11.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.950][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:48:11.951][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:48:11.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.955][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:48:11.956][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:48:11.960][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:48:11.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.964][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:48:11.965][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:48:11.966][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:48:11.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:11.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:11.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:11.970][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:48:11.971][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:11.972][self$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 18:48:11.973][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:11.974][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:11.975][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:11.976][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:11.978][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:11.979][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:11.980][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:48:11.981][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:11.982][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:11.983][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:48:11.984][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:11.985][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:11.985][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:11.986][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:48:11.986][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:48:11.986][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:48:11.986][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:48:11.986][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:48:11.988][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:11.989][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:11.989][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:11.990][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:11.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:11.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:11.993][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:11.994][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:11.995][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:11.996][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:11.997][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:11.998][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:11.999][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:48:12.001][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.002][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:48:12.003][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.004][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:12.005][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.006][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.007][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.009][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:48:12.010][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:12.012][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.013][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:48:12.014][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:12.015][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.016][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.017][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:48:12.017][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:48:12.017][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:48:12.017][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:48:12.017][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:48:12.018][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:12.019][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:12.020][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:12.021][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:12.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:12.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:12.024][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.025][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.026][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:12.027][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:12.028][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.029][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.030][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:48:12.032][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.033][self$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 18:48:12.034][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.035][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:12.037][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.038][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.039][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.040][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.041][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:48:12.042][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:12.043][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.044][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:48:12.045][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:12.046][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.047][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.048][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.049][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:12.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:12.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:12.052][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:12.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:12.064][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:12.065][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.067][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.068][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:12.069][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:12.070][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.071][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.072][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:48:12.074][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.075][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:48:12.076][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.077][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:12.079][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.080][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.081][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.082][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.083][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:48:12.084][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:12.085][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.085][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:48:12.087][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:12.087][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.088][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.089][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.090][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:48:12.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:12.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:12.093][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:12.094][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:12.095][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:12.096][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.097][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.098][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:12.099][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:12.099][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.100][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:48:12.102][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:48:12.103][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.108][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 18:48:12.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.110][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 18:48:12.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.123][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 18:48:12.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.136][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 18:48:12.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.155][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 18:48:12.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.158][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 18:48:12.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.159][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.DEBUG[2022-10-18 18:48:12.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.162][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 18:48:12.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.168][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 18:48:12.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.178][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:48:12.180][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:48:12.181][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:48:12.183][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:48:12.184][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:48:12.185][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:48:12.187][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:48:12.188][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:48:12.190][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:48:12.191][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:48:12.192][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:48:12.194][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:48:12.195][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:48:12.197][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:48:12.198][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:48:12.199][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:48:12.201][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:48:12.202][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:48:12.203][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:48:12.205][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:48:12.206][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:48:12.207][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:48:12.209][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:48:12.210][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:48:12.211][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:48:12.213][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:48:12.214][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:48:12.216][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:48:12.217][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:48:12.219][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:48:12.220][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:48:12.221][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:48:12.223][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:48:12.224][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:48:12.225][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:48:12.227][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:48:12.228][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:48:12.229][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:48:12.231][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:48:12.232][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:48:12.233][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:48:12.235][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:48:12.236][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:48:12.237][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:48:12.239][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:48:12.240][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:48:12.242][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:48:12.243][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:48:12.244][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:48:12.246][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:48:12.247][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:48:12.248][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:48:12.250][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:48:12.251][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:48:12.253][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:48:12.254][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:48:12.255][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:48:12.257][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:48:12.258][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:48:12.260][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:48:12.261][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:48:12.262][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:48:12.264][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:48:12.265][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:48:12.266][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:48:12.268][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:48:12.269][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:48:12.270][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:48:12.272][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:48:12.273][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:48:12.274][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:48:12.276][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:48:12.277][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:48:12.278][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:48:12.280][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:48:12.281][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:48:12.282][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:48:12.283][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:48:12.285][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:48:12.286][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:48:12.287][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:48:12.288][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:48:12.290][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:48:12.291][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:48:12.293][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:48:12.293][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:48:12.294][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.295][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 18:48:12.296][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.297][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 18:48:12.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.308][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 18:48:12.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.312][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 18:48:12.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.318][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 18:48:12.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.320][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 18:48:12.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.326][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 18:48:12.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.331][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 18:48:12.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.337][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 18:48:12.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.345][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 18:48:12.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.350][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 18:48:12.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.356][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 18:48:12.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.377][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.DEBUG[2022-10-18 18:48:12.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.382][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 18:48:12.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.403][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 18:48:12.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.407][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 18:48:12.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:48:12.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.413][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 18:48:12.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.416][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-10-18 18:48:12.418][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-10-18 18:48:12.419][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.420][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.421][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.422][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:48:12.423][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.424][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.425][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.426][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-10-18 18:48:12.427][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-10-18 18:48:12.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:48:12.429][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.430][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-10-18 18:48:12.431][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-10-18 18:48:12.432][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-10-18 18:48:12.433][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:48:12.434][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:48:12.434][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:48:12.434][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:48:12.435][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-18 18:48:12.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:12.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:12.438][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:48:12.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:48:12.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:48:12.441][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:48:12.442][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:48:12.442][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-10-18 18:48:12.443][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:48:12.444][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:48:12.445][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:48:12.446][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-10-18 18:48:12.446][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-10-18 18:48:12.447][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:48:12.449][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:48:12.451][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-10-18 18:48:12.453][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:48:12.454][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:48:12.456][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:48:12.459][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-10-18 18:48:12.460][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-10-18 18:48:12.461][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-10-18 18:48:12.463][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-10-18 18:48:12.464][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:48:12.465][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-18 18:48:12.466][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-10-18 18:48:12.467][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-10-18 18:48:12.469][biodb::testThat]
biodb.INFO [2022-10-18 18:48:12.470][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2022-10-18 18:48:12.471][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:12.472][biodb::testThat]
biodb.DEBUG[2022-10-18 18:48:12.475][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-10-18 18:48:12.479][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:48:12.481][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-10-18 18:48:12.482][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:48:12.484][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-10-18 18:48:12.488][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-10-18 18:48:12.491][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:48:12.492][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2022-10-18 18:48:12.493][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:48:12.495][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2022-10-18 18:48:12.498][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2022-10-18 18:48:12.499][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:48:12.501][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2022-10-18 18:48:12.502][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:48:12.503][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:48:12.504][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:48:12.506][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-10-18 18:48:12.507][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:48:12.508][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:48:12.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:12.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:12.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:12.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:12.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:12.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:12.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:12.523][scheduler$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 18:48:12.526][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:12.527][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:12.528][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2022-10-18 18:48:13.047][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2022-10-18 18:48:13.849][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:13.862][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2022-10-18 18:48:13.882][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2022-10-18 18:48:13.901][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2022-10-18 18:48:13.910][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:48:13.940][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:48:13.944][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-10-18 18:48:13.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:13.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:13.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:13.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:13.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:13.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:13.967][FUN] Functions in observer BiodbConfig: [21]: ".__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 18:48:13.971][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:13.973][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:13.975][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:13.976][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:13.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:13.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:13.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:13.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:13.987][ef$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:48:13.988][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:48:13.989][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:13.990][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.016][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-10-18 18:48:14.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-10-18 18:48:14.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.039][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:48:14.041][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:48:14.042][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.043][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.045][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:48:14.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:48:14.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-18 18:48:14.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-18 18:48:14.054][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.055][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.056][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-18 18:48:14.057][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-18 18:48:14.058][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.059][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.061][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:14.062][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:14.063][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.064][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.065][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:14.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:14.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.073][ef$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:48:14.074][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:48:14.075][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.076][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.077][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-10-18 18:48:14.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:48:14.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.085][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:14.086][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:14.087][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.088][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:14.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.097][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:14.098][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:14.099][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.100][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:14.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:14.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.110][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:48:14.111][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:48:14.112][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.113][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.114][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-10-18 18:48:14.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-10-18 18:48:14.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.121][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:48:14.122][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:48:14.123][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.124][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-10-18 18:48:14.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-10-18 18:48:14.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:14.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:14.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:14.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:14.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:14.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:14.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:14.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:14.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:14.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:14.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:14.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:14.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:14.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:14.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:14.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:14.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:14.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:14.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:14.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:14.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:14.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:14.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:48:14.184][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2022-10-18 18:48:14.186][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:48:14.188][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-10-18 18:48:14.190][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-10-18 18:48:14.191][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:48:14.192][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:14.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:14.195][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:14.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:14.196][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:14.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
> 
> proc.time()
   user  system elapsed 
 23.820   1.103  75.107

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.1990.2234.061
ChebiEntry0.3640.0000.364