Multiple platform build/check report for BioC 3.20 - CHECK results for biodbChebi on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4461
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4716
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4466
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4498
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4446
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4445
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 lconway

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

raw results

Summary

Package: biodbChebi

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.11.0.tar.gz

StartedAt: 2024-10-02 19:11:17 -0400 (Wed, 02 Oct 2024)

EndedAt: 2024-10-02 19:13:31 -0400 (Wed, 02 Oct 2024)

EllapsedTime: 134.4 seconds

RetCode: 0

Status: OK

CheckDir: biodbChebi.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 3.085  1.232   8.546
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-10-02 19:12:27.024][biodb::testContext]
biodb.INFO [2024-10-02 19:12:27.029][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 19:12:27.030][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-02 19:12:27.032][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 19:12:27.033][biodb::testContext]
biodb.INFO [2024-10-02 19:12:27.041][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-10-02 19:12:27.044][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-02 19:12:27.054][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:12:27.056][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-02 19:12:27.058][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-02 19:12:27.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.064][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-02 19:12:27.088][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-02 19:12:27.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.093][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-02 19:12:27.095][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-02 19:12:27.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.099][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-02 19:12:27.101][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-02 19:12:27.102][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-02 19:12:27.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.123][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-02 19:12:27.124][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-02 19:12:27.126][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-02 19:12:27.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.131][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-02 19:12:27.132][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-02 19:12:27.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.137][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-02 19:12:27.139][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-02 19:12:27.140][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-02 19:12:27.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.145][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-02 19:12:27.146][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-02 19:12:27.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.149][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-02 19:12:27.150][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-02 19:12:27.152][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-02 19:12:27.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.157][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-02 19:12:27.158][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-02 19:12:27.159][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-02 19:12:27.160][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-02 19:12:27.162][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-02 19:12:27.163][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-02 19:12:27.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.168][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-02 19:12:27.169][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-02 19:12:27.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.174][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-02 19:12:27.175][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-02 19:12:27.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.179][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-02 19:12:27.180][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-02 19:12:27.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.185][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-02 19:12:27.186][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-02 19:12:27.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.190][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-02 19:12:27.192][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-02 19:12:27.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.196][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-02 19:12:27.198][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-02 19:12:27.224][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-02 19:12:27.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.228][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-02 19:12:27.230][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-02 19:12:27.231][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-02 19:12:27.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.239][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-02 19:12:27.282][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.301][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-02 19:12:27.302][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.304][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:12:27.305][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.306][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.307][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.308][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.310][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 19:12:27.311][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:12:27.312][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.313][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-02 19:12:27.314][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:12:27.316][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.316][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.318][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:12:27.318][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:12:27.318][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:12:27.318][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 19:12:27.318][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 19:12:27.319][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:12:27.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.322][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:12:27.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.327][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.328][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.329][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:12:27.330][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:12:27.332][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.333][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.334][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-02 19:12:27.336][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.338][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 19:12:27.339][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:12:27.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.343][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.344][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.346][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.347][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 19:12:27.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:12:27.350][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.351][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-02 19:12:27.352][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:12:27.354][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.355][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.357][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:12:27.357][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:12:27.357][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:12:27.357][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 19:12:27.357][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 19:12:27.359][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:12:27.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.363][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:12:27.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.366][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.368][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.369][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:12:27.371][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:12:27.372][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.373][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.374][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-02 19:12:27.377][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.378][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-02 19:12:27.379][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.381][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:12:27.382][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.384][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.385][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.386][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.388][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 19:12:27.389][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:12:27.391][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.392][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-02 19:12:27.401][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:12:27.403][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.404][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.406][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.408][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:12:27.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.410][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:12:27.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.414][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.415][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.417][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:12:27.418][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:12:27.419][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.420][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.422][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-02 19:12:27.424][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.425][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 19:12:27.426][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.427][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:12:27.429][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.430][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.431][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.433][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.434][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 19:12:27.436][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:12:27.438][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.439][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-02 19:12:27.440][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:12:27.441][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.442][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.444][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.445][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:12:27.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.449][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:12:27.450][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.452][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.453][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.454][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:12:27.456][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:12:27.457][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.458][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:12:27.463][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:12:27.464][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.470][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.DEBUG[2024-10-02 19:12:27.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.563][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-02 19:12:27.569][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-02 19:12:27.571][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-02 19:12:27.573][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-02 19:12:27.575][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 19:12:27.577][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-02 19:12:27.579][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-02 19:12:27.581][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-02 19:12:27.583][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-02 19:12:27.585][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-02 19:12:27.587][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 19:12:27.589][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-02 19:12:27.591][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-02 19:12:27.593][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-02 19:12:27.595][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-02 19:12:27.597][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-02 19:12:27.599][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-02 19:12:27.601][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-02 19:12:27.603][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 19:12:27.605][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-02 19:12:27.607][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-02 19:12:27.608][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-02 19:12:27.610][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-02 19:12:27.612][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-02 19:12:27.614][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-02 19:12:27.616][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-02 19:12:27.618][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-02 19:12:27.620][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-02 19:12:27.622][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-02 19:12:27.624][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-02 19:12:27.626][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-02 19:12:27.628][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-02 19:12:27.630][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-02 19:12:27.632][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-02 19:12:27.634][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-02 19:12:27.636][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-02 19:12:27.637][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-02 19:12:27.638][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-02 19:12:27.640][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-02 19:12:27.642][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-02 19:12:27.644][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-02 19:12:27.646][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-02 19:12:27.648][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-02 19:12:27.650][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-02 19:12:27.652][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-02 19:12:27.653][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-02 19:12:27.655][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-02 19:12:27.666][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-02 19:12:27.668][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-02 19:12:27.670][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-02 19:12:27.672][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-02 19:12:27.674][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-02 19:12:27.677][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-02 19:12:27.679][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-02 19:12:27.680][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-02 19:12:27.682][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-02 19:12:27.684][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-02 19:12:27.686][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-02 19:12:27.688][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-02 19:12:27.690][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-02 19:12:27.692][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-02 19:12:27.694][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-02 19:12:27.696][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-02 19:12:27.698][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-02 19:12:27.699][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-02 19:12:27.701][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-02 19:12:27.703][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 19:12:27.704][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 19:12:27.706][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-02 19:12:27.708][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-02 19:12:27.709][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-02 19:12:27.711][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-02 19:12:27.713][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-02 19:12:27.715][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-02 19:12:27.717][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-02 19:12:27.719][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-02 19:12:27.721][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-02 19:12:27.722][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-02 19:12:27.724][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-02 19:12:27.726][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-02 19:12:27.727][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-02 19:12:27.728][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-02 19:12:27.730][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-02 19:12:27.737][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-02 19:12:27.739][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-10-02 19:12:27.744][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:12:27.745][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.748][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.828][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[2024-10-02 19:12:27.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.882][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[2024-10-02 19:12:27.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:12:27.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:27.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:27.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:27.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:27.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:27.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:27.893][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-02 19:12:27.908][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-02 19:12:27.918][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.920][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.921][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.923][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:12:27.924][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.925][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.927][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.928][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-02 19:12:27.930][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-02 19:12:27.931][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:12:27.933][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.934][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-02 19:12:27.935][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-02 19:12:27.937][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-02 19:12:27.938][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-02 19:12:27.940][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:12:27.940][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:12:27.940][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:12:27.941][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-02 19:12:27.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.944][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:12:27.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:12:27.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:12:27.947][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:12:27.948][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:27.948][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-02 19:12:27.950][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:12:27.950][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:12:27.952][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-02 19:12:27.953][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-02 19:12:27.953][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-02 19:12:27.961][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 19:12:27.962][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 19:12:27.964][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-02 19:12:27.966][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 19:12:27.968][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 19:12:27.970][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 19:12:28.005][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-02 19:12:28.007][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-02 19:12:28.013][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-02 19:12:28.018][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-02 19:12:28.024][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 19:12:28.025][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 19:12:28.027][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-02 19:12:28.028][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-02 19:12:28.042][biodb::testThat]
biodb.INFO [2024-10-02 19:12:28.044][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-02 19:12:28.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:28.046][biodb::testThat]
biodb.TRACE[2024-10-02 19:12:28.051][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-10-02 19:12:28.053][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:28.057][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:28.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:28.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:28.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:28.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:28.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:28.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:28.096][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[2024-10-02 19:12:28.109][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.111][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.114][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.140][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:28.142][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:28.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.145][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.183][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:28.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:28.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.189][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:28.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:28.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.193][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:28.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:28.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.201][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:28.202][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:28.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.205][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:28.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:28.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.225][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:28.226][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:28.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.229][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:28.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:28.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.236][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:28.237][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:28.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.240][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.241][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:28.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:28.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.247][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:28.248][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.251][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.253][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:28.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.258][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.259][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.262][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.269][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:28.271][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:28.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.273][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:28.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:28.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.280][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:28.282][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.284][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:28.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.291][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:28.292][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:28.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.295][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.297][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:28.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:28.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:28.403][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-10-02 19:12:28.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:28.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:28.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:28.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:28.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:28.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:28.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:28.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:28.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.511][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 19:12:28.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 19:12:28.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.517][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 19:12:28.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 19:12:28.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-02 19:12:28.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-02 19:12:28.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.528][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-02 19:12:28.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-02 19:12:28.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.670][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.672][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.674][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:28.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:28.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.716][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.717][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.720][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:28.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:28.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:28.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:28.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:28.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:28.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:28.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.755][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:28.756][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:28.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.758][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:28.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:28.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.778][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:28.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:28.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.784][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:28.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:28.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.790][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:28.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:28.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.794][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:28.795][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:28.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.797][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.798][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:28.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:28.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.833][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.834][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.837][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:28.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.875][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.876][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.879][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:28.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.898][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:28.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:28.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.904][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:28.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:28.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.911][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:28.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:28.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.916][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:28.918][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:28.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.920][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.922][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:28.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:28.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.947][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.954][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.959][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.965][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.966][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.968][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.970][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:28.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.986][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:28.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:28.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.992][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:28.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:28.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:28.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:28.997][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:28.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.003][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.004][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.007][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.008][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:29.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:29.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.030][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:29.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:29.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:29.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:29.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.041][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:29.043][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:29.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.045][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.046][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:29.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:29.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.079][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.080][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.083][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:29.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:29.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:29.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:29.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:29.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:29.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.118][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:29.120][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:29.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.122][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:29.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:29.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.156][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.158][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.161][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.169][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:29.171][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:29.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.174][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.181][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:29.190][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:29.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.192][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.200][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:29.201][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:29.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.204][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.210][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.212][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.214][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.221][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.222][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.233][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:29.234][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:29.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.236][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.243][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:29.244][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:29.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.247][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.255][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 19:12:29.256][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:29.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.259][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.266][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:29.268][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:29.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.270][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.276][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:29.277][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:29.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.280][ef$get] fields variable is a list.
biodb.INFO [2024-10-02 19:12:29.292][biodb::testThat]
biodb.INFO [2024-10-02 19:12:29.293][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-02 19:12:29.295][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:29.296][biodb::testThat]
biodb.DEBUG[2024-10-02 19:12:29.314][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-10-02 19:12:29.323][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:29.328][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-10-02 19:12:29.329][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:12:29.332][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-10-02 19:12:29.333][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:29.365][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:29.367][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:29.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:29.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:29.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:29.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:29.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:29.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:29.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:29.384][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.386][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.388][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.424][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:29.426][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:29.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.429][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.430][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:29.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:29.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.435][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:29.436][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:29.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.439][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.441][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:29.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:29.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.446][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:29.447][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:29.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.450][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:29.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:29.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.457][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.458][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.461][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:29.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.467][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.469][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.471][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.472][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:29.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.478][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:29.479][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:29.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.482][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.483][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:29.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:29.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.489][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:29.490][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:29.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.493][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:29.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:29.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.500][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:29.502][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:29.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.504][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:29.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:29.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.511][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:29.512][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:29.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.514][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.516][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:29.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:29.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.521][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:29.523][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:29.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.525][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:29.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:29.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:29.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:29.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:29.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:29.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:29.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:29.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:29.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:29.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:29.586][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-10-02 19:12:29.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-02 19:12:29.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-02 19:12:29.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-02 19:12:29.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-02 19:12:29.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-02 19:12:29.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-02 19:12:29.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 19:12:29.621][biodb::testThat]
biodb.INFO [2024-10-02 19:12:29.623][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-02 19:12:29.624][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:29.625][biodb::testThat]
biodb.TRACE[2024-10-02 19:12:29.630][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:29.631][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:29.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.633][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:29.635][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-10-02 19:12:29.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:29.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:29.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:29.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:29.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:29.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:29.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:29.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:29.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:29.688][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-10-02 19:12:29.694][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-02 19:12:29.720][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:12:29.741][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-02 19:12:29.743][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:12:29.745][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-02 19:12:29.777][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:12:29.782][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:29.784][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:29.786][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:12:30.451][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:12:30.946][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:30.949][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-10-02 19:12:30.971][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-10-02 19:12:30.974][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-10-02 19:12:30.995][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:30.997][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:30.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.000][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.002][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.004][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.008][ef$get] fields variable is a list.
biodb.INFO [2024-10-02 19:12:31.028][biodb::testThat]
biodb.INFO [2024-10-02 19:12:31.030][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-02 19:12:31.031][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:31.033][biodb::testThat]
biodb.TRACE[2024-10-02 19:12:31.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:31.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:31.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:31.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:31.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.077][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:31.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:31.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:31.155][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:12:31.160][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:12:31.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 19:12:31.164][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:12:31.166][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-10-02 19:12:31.197][biodb::testThat]
biodb.INFO [2024-10-02 19:12:31.198][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-02 19:12:31.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:31.201][biodb::testThat]
biodb.TRACE[2024-10-02 19:12:31.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:31.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:31.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:31.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:31.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:31.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:31.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:31.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:31.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.263][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 19:12:31.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 19:12:31.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.268][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 19:12:31.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 19:12:31.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.272][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-02 19:12:31.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-02 19:12:31.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.277][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-02 19:12:31.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-02 19:12:31.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:31.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:31.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:31.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:31.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.318][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:31.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:31.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:31.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:31.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:31.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 19:12:31.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 19:12:31.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.350][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 19:12:31.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 19:12:31.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.355][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-02 19:12:31.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-02 19:12:31.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:31.359][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-02 19:12:31.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-02 19:12:31.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:31.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 19:12:31.372][biodb::testThat]
biodb.INFO [2024-10-02 19:12:31.373][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-02 19:12:31.375][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:31.376][biodb::testThat]
biodb.INFO [2024-10-02 19:12:31.388][biodb::testThat]
biodb.INFO [2024-10-02 19:12:31.390][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-02 19:12:31.391][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:31.393][biodb::testThat]
biodb.INFO [2024-10-02 19:12:31.405][biodb::testThat]
biodb.INFO [2024-10-02 19:12:31.407][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-02 19:12:31.409][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:31.410][biodb::testThat]
biodb.DEBUG[2024-10-02 19:12:31.416][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-10-02 19:12:31.911][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-10-02 19:12:32.957][biodb::testThat]
biodb.INFO [2024-10-02 19:12:32.958][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-02 19:12:32.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:32.961][biodb::testThat]
biodb.DEBUG[2024-10-02 19:12:33.329][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-10-02 19:12:33.699][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:33.701][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:33.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:33.703][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:33.704][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:33.705][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:33.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:33.708][ef$get] fields variable is a list.
biodb.INFO [2024-10-02 19:12:33.710][biodb::testThat]
biodb.INFO [2024-10-02 19:12:33.711][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-10-02 19:12:33.712][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:12:33.713][biodb::testThat]
biodb.TRACE[2024-10-02 19:12:33.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:33.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:33.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:33.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:33.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:33.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:33.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:33.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:33.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:33.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:33.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:33.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:33.862][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:12:33.867][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:12:33.869][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 19:12:33.871][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:12:33.873][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-02 19:12:33.964][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:12:33.968][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:12:33.970][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 19:12:33.972][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:12:33.974][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-10-02 19:12:33.995][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-02 19:12:33.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-02 19:12:33.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:33.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:34.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:34.045][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:12:34.049][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:12:34.051][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-02 19:12:34.053][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:12:34.056][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-02 19:12:34.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:34.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:34.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:34.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:34.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:34.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:34.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:34.075][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-10-02 19:12:34.142][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:34.145][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-10-02 19:12:34.146][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:34.148][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:34.149][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:34.151][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:34.152][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:34.153][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:34.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:34.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:34.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:34.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:34.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:34.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:34.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:34.172][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-10-02 19:12:34.195][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:34.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:34.217][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-10-02 19:12:34.561][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-10-02 19:12:34.899][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:34.903][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-10-02 19:12:34.908][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-10-02 19:12:34.912][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-10-02 19:12:34.914][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:34.916][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:34.918][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:34.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:34.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:34.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:34.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:34.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:34.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:34.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:34.945][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:34.946][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:34.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.949][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:34.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:34.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.954][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:34.955][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:34.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.957][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.958][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:34.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:34.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.963][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:34.965][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:34.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.967][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.970][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:34.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:34.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.976][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:34.977][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:34.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:34.992][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:34.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:34.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:35.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.004][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:35.006][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:35.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.008][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.010][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:35.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:35.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.015][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:35.017][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:35.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.019][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.021][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:35.023][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.025][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.027][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:35.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.033][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:35.034][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:35.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.036][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:35.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:35.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.042][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:35.044][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:35.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.046][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:35.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:35.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.053][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:35.054][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:35.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.056][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.058][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:35.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:35.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.063][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:35.064][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:35.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.066][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.067][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:35.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:35.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:35.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:35.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:35.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:35.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:35.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:35.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:35.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:35.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:35.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:35.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:35.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:35.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:35.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:35.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:35.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:35.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:35.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:35.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:35.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:35.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:35.130][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-10-02 19:12:35.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:35.157][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:12:35.161][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:12:35.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-02 19:12:35.164][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:12:35.166][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-02 19:12:35.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:35.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:35.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:35.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:35.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:35.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:35.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:35.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:35.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:35.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:35.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:35.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:35.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:35.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:35.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:35.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:35.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:35.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:35.241][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-10-02 19:12:35.243][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:35.245][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-10-02 19:12:35.247][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:35.249][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:35.250][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:35.252][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:35.253][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:35.254][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:35.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:35.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:35.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:35.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:35.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:35.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:35.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:35.288][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-10-02 19:12:35.292][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:35.293][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:35.295][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-10-02 19:12:35.638][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-10-02 19:12:35.973][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:35.975][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-10-02 19:12:35.980][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-10-02 19:12:35.984][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-10-02 19:12:35.986][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:35.988][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:35.989][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:35.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:35.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:35.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:36.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:36.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:36.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:36.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:36.007][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:36.008][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:36.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.010][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:36.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:36.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.017][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:36.018][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:36.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.020][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.022][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:36.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:36.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.027][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:36.028][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:36.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.031][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.033][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:36.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:36.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.039][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:36.040][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:36.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.043][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:36.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:36.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.050][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:36.052][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:36.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.054][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:36.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:36.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.061][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:36.062][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:36.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.077][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.079][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:36.080][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.083][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.084][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:36.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.088][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:36.089][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:36.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.091][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:36.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:36.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.097][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:36.098][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:36.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.101][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:36.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:36.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.110][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:36.111][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:36.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.113][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.115][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:36.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:36.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.119][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:36.120][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:36.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.122][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.123][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:36.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:36.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:36.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:36.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:36.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:36.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:36.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:36.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:36.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:36.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:36.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:36.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:36.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:36.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:36.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:36.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:36.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:36.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:36.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:36.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:36.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:36.198][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-10-02 19:12:36.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:36.246][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:12:36.250][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:12:36.252][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 19:12:36.254][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:12:36.256][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-02 19:12:36.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:36.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:36.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:36.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:36.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:36.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:36.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:36.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:36.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:36.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:36.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:36.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:36.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:36.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:36.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:36.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:36.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:36.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:36.305][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-10-02 19:12:36.306][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:36.307][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-10-02 19:12:36.308][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:36.310][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:36.311][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:36.313][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:36.314][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:36.314][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:36.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:36.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:36.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:36.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:36.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:36.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:36.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:36.333][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-10-02 19:12:36.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:36.338][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:36.339][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-10-02 19:12:36.985][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-10-02 19:12:37.341][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:37.359][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-10-02 19:12:37.364][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-10-02 19:12:37.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-10-02 19:12:37.370][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:37.371][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:37.373][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:37.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:37.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:37.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:37.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:37.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:37.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:37.389][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.TRACE[2024-10-02 19:12:37.393][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:37.395][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:37.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.397][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:37.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:37.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.404][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:37.405][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:37.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.407][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.418][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:37.419][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:37.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.422][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.424][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:37.426][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:37.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.428][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:37.432][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:37.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.434][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.435][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:37.436][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:37.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.438][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.440][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:37.441][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.443][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.445][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:37.446][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:37.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.448][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.449][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:37.450][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:37.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.452][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:37.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:37.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.458][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:37.459][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:37.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.461][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.463][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:37.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:37.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.467][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:37.468][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:37.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.470][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:37.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:37.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:37.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:37.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:37.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:37.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:37.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:37.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:37.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:37.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:37.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:37.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:37.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:37.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:37.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:37.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:37.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:37.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:37.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:37.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:37.518][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-10-02 19:12:37.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:37.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:37.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:37.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:37.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:37.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:37.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:37.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:37.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:37.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:37.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:37.565][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-10-02 19:12:37.566][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:37.568][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-10-02 19:12:37.569][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:37.571][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:37.572][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:37.573][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:37.575][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:37.576][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:37.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:37.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:37.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:37.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:37.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:37.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:37.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:37.590][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-10-02 19:12:37.593][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:37.595][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:37.613][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-10-02 19:12:37.950][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-10-02 19:12:38.285][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:38.287][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-10-02 19:12:38.292][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-10-02 19:12:38.295][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-10-02 19:12:38.297][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:38.299][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:38.301][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:38.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:38.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:38.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:38.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:38.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:38.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:38.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:38.319][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:38.320][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:38.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.322][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:38.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:38.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.327][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:38.328][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:38.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.330][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.331][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:38.332][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:38.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.335][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.336][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:38.338][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:38.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.340][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.342][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:38.343][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:38.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.344][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.345][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:38.346][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:38.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.348][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.349][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:38.350][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.353][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.354][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:38.356][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:38.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.358][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.360][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:38.362][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:38.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.364][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:38.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:38.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.372][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:38.383][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:38.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.386][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.388][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:38.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:38.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.394][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:38.395][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:38.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.397][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:38.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:38.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:38.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:38.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:38.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:38.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:38.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:38.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:38.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:38.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:38.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:38.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:38.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:38.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:38.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:38.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:38.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:38.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:38.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:38.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:38.467][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-10-02 19:12:38.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:38.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:38.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:38.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:38.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:38.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:38.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:38.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:38.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:38.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:38.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:38.527][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-10-02 19:12:38.528][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:38.530][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-10-02 19:12:38.531][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:38.532][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:38.533][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:38.533][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:38.534][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:38.535][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:38.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:38.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:38.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:38.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:38.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:38.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:38.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:38.551][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-10-02 19:12:38.554][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:38.555][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:38.590][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-10-02 19:12:38.930][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-10-02 19:12:39.264][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:39.267][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-10-02 19:12:39.272][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-10-02 19:12:39.276][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-10-02 19:12:39.278][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:39.280][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:39.282][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:39.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:39.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:39.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:39.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:39.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:39.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:39.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:39.299][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:39.301][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:39.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.303][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:39.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:39.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.311][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:39.312][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:39.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.315][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.316][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:39.318][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:39.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.320][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.323][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:39.325][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:39.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.328][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.329][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:39.331][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:39.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.333][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:39.336][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:39.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.339][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.340][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:39.342][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.344][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.345][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:39.347][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:39.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.349][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.351][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:39.352][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:39.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.354][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:39.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:39.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.361][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:39.362][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:39.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.364][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.365][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:39.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:39.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.371][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:39.372][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:39.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.374][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:39.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:39.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:39.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:39.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:39.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:39.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:39.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:39.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:39.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:39.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:39.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:39.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:39.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:39.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:39.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:39.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:39.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:39.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:39.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:39.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:39.437][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-10-02 19:12:39.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:39.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:39.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:39.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:39.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:39.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:39.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:39.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:39.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:39.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:39.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:39.467][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-10-02 19:12:39.468][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:39.470][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-10-02 19:12:39.471][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:39.472][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:39.473][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:39.474][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:39.475][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:39.476][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:39.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:39.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:39.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:39.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:39.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:39.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:39.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:39.491][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-10-02 19:12:39.494][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:39.496][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:39.497][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-10-02 19:12:39.829][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-10-02 19:12:40.168][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:40.171][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-10-02 19:12:40.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-10-02 19:12:40.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-10-02 19:12:40.181][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:40.183][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:40.184][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:40.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:40.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:40.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:40.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:40.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:40.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:40.197][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.TRACE[2024-10-02 19:12:40.200][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:40.201][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:40.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.203][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:40.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:40.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.209][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:40.210][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:40.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.213][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.214][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:40.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:40.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.229][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:40.231][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:40.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.232][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:40.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:40.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.239][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:40.240][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:40.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.243][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:40.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:40.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.262][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:40.263][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:40.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.264][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:40.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:40.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.269][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:40.270][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:40.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.272][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.273][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:40.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:40.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.278][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:40.279][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:40.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.282][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.283][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:40.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:40.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.287][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:40.288][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:40.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.291][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:40.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:40.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.298][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:40.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:40.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.301][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:40.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:40.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.307][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:40.308][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:40.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.310][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.312][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:40.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:40.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.317][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:40.318][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:40.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.320][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.322][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:40.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:40.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:40.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:40.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:40.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:40.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:40.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:40.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:40.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:40.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:40.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:40.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:40.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:40.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:40.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:40.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:40.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:40.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:40.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:40.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:40.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:40.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:40.395][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-10-02 19:12:40.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:40.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:40.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:40.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:40.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:40.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:40.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:40.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:40.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:40.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:40.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:40.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:40.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:40.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:40.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:40.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:40.431][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-10-02 19:12:40.434][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:40.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-10-02 19:12:40.438][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:40.440][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:40.441][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:40.442][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:40.443][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:40.444][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:40.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:40.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:40.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:40.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:40.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:40.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:40.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:40.461][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-10-02 19:12:40.464][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:40.465][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:40.467][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-10-02 19:12:40.817][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-10-02 19:12:41.152][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:41.156][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-10-02 19:12:41.161][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-10-02 19:12:41.164][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-10-02 19:12:41.166][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:41.167][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:41.168][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:41.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:41.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:41.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:41.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:41.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:41.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:41.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:41.185][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:41.187][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:41.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.189][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:41.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:41.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.194][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:41.195][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:41.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.201][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.203][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:41.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:41.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.210][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:41.211][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:41.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.214][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.216][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:41.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:41.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.221][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:41.223][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:41.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.237][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:41.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:41.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.243][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:41.244][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:41.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.245][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:41.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:41.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.250][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:41.252][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:41.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.254][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.255][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:41.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.260][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:41.261][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:41.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.263][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.264][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:41.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:41.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.267][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:41.269][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:41.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.271][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:41.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:41.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.277][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:41.278][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:41.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.281][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:41.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:41.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.288][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:41.289][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:41.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.290][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.292][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:41.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:41.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.297][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:41.298][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:41.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.300][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.301][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:41.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:41.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:41.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:41.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:41.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:41.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:41.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:41.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:41.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:41.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:41.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:41.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:41.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:41.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:41.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:41.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:41.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:41.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:41.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:41.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:41.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:41.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:41.369][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-10-02 19:12:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:41.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:41.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:41.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:41.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:41.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:41.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:41.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:41.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:41.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:41.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:41.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:41.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:41.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:41.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:41.402][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-10-02 19:12:41.403][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:41.405][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-10-02 19:12:41.406][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:41.423][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:41.424][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:41.425][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:41.427][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:41.428][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:41.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:41.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:41.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:41.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:41.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:41.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:41.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:41.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-10-02 19:12:41.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:41.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:41.450][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-10-02 19:12:41.790][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-10-02 19:12:42.133][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:42.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-10-02 19:12:42.142][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-10-02 19:12:42.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-10-02 19:12:42.153][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:42.155][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:42.156][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:42.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:42.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:42.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:42.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:42.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:42.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:42.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:42.178][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:42.180][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:42.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.182][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:42.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:42.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.188][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:42.189][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:42.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.192][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.193][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:42.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:42.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.199][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:42.200][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:42.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.202][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:42.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:42.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.208][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:42.210][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:42.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.214][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:42.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:42.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.221][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:42.222][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:42.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:42.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:42.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.232][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:42.244][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:42.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.246][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.248][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:42.249][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:42.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.252][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.254][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:42.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:42.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.258][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:42.259][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:42.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.261][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:42.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:42.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.268][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:42.269][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:42.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.271][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.273][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:42.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:42.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.279][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:42.285][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:42.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.289][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.291][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:42.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:42.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.297][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:42.299][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:42.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.302][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.307][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:42.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:42.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:42.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:42.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:42.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:42.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:42.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:42.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:42.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:42.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:42.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:42.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:42.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:42.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:42.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:42.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:42.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:42.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:42.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:42.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:42.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:42.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:42.370][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-10-02 19:12:42.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:42.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:42.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:42.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:42.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:42.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:42.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:42.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:42.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:42.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:42.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:42.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:42.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:42.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:42.405][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-10-02 19:12:42.406][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:42.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-10-02 19:12:42.417][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:42.418][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:42.420][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:42.421][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:42.422][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:42.424][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:42.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:42.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:42.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:42.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:42.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:42.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:42.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:42.447][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-10-02 19:12:42.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:42.453][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:42.455][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-10-02 19:12:42.796][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-10-02 19:12:43.218][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:43.221][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-10-02 19:12:43.227][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-10-02 19:12:43.232][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-10-02 19:12:43.235][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:43.237][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:43.239][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:43.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:43.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:43.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:43.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:43.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:43.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:43.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:43.268][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:43.270][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:43.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.274][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:43.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:43.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.283][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:43.285][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:43.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.287][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.289][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:43.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:43.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.294][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:43.296][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:43.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.298][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.300][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:43.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:43.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.305][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:43.306][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:43.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.308][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:43.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:43.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.316][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:43.317][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:43.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.320][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:43.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:43.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:43.336][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:43.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.339][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.341][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:43.342][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:43.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.345][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.347][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:43.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:43.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.355][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:43.360][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:43.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.363][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:43.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:43.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.383][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:43.385][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:43.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.388][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.390][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:43.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:43.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.396][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:43.397][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:43.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.400][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.401][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:43.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:43.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.411][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:43.413][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:43.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.416][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:43.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:43.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:43.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:43.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:43.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:43.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:43.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:43.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:43.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:43.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:43.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:43.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:43.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:43.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:43.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:43.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:43.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:43.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:43.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:43.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:43.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:43.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:43.482][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-10-02 19:12:43.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:43.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:43.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:43.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:43.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:43.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:43.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:43.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:43.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:43.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:43.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:43.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:43.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:43.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:43.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:43.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:43.521][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-10-02 19:12:43.522][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:43.525][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-10-02 19:12:43.526][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:43.527][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:43.528][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:43.530][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:43.531][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:43.532][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:43.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:43.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:43.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:43.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:43.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:43.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:43.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:43.567][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-10-02 19:12:43.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:43.573][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:43.575][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-10-02 19:12:43.921][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-10-02 19:12:44.258][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:44.261][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-10-02 19:12:44.273][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-10-02 19:12:44.277][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-10-02 19:12:44.281][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:44.282][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:44.284][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:44.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:44.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:44.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:44.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:44.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:44.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:44.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:44.306][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:44.307][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:44.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.310][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:44.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:44.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.317][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:44.319][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:44.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.327][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.329][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:44.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:44.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.335][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:44.336][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:44.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.339][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:44.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:44.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.349][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:44.351][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:44.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.354][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:44.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:44.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.360][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:44.361][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:44.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.364][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:44.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:44.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.371][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:44.372][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:44.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.374][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.376][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:44.377][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:44.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.380][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.381][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:44.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:44.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.387][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:44.389][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:44.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.391][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:44.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:44.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.397][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:44.399][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:44.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.401][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:44.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:44.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.417][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:44.418][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:44.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.421][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.423][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:44.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:44.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.442][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:44.444][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:44.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.446][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.448][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:44.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:44.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:44.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:44.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:44.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:44.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:44.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:44.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:44.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:44.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:44.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:44.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:44.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:44.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:44.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:44.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:44.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:44.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:44.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:44.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:44.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:44.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:44.508][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-10-02 19:12:44.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:44.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:44.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:44.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:44.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:44.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:44.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:44.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:44.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:44.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:44.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:44.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:44.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:44.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:44.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:44.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:44.540][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-10-02 19:12:44.541][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:44.543][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-10-02 19:12:44.545][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:44.546][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:44.547][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:44.549][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:44.550][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:44.551][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:44.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:44.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:44.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:44.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:44.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:44.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:44.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:44.567][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-10-02 19:12:44.573][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:44.574][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:44.576][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-10-02 19:12:44.916][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-10-02 19:12:45.256][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:45.260][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-10-02 19:12:45.267][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-10-02 19:12:45.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-10-02 19:12:45.289][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:45.291][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:45.294][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:45.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:45.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:45.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:45.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:45.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:45.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:45.313][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[2024-10-02 19:12:45.316][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:45.318][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:45.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.321][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:45.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:45.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.329][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:45.331][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:45.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.336][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.338][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:45.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:45.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.344][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:45.345][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:45.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.348][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.350][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:45.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:45.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.355][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:45.357][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:45.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.359][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:45.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:45.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.365][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:45.366][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:45.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.369][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:45.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:45.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.376][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:45.378][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:45.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.382][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.384][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:45.386][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:45.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.388][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.390][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:45.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:45.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.399][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:45.401][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:45.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.403][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:45.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:45.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.412][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:45.413][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:45.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.414][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:45.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:45.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.425][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:45.426][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:45.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.428][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.430][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:45.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:45.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.435][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:45.436][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:45.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.439][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.441][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:45.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:45.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:45.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:45.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:45.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:45.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:45.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:45.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:45.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:45.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:45.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:45.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:45.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:45.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:45.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:45.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:45.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:45.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:45.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:45.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:45.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:45.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:45.517][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-10-02 19:12:45.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:45.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:45.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:45.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:45.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:45.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:45.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:45.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:45.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:45.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:45.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:45.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:45.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:45.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:45.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:45.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:45.551][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-10-02 19:12:45.552][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:45.555][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-10-02 19:12:45.557][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:45.559][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:45.560][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:45.562][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:45.564][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:45.566][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:45.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:45.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:45.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:45.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:45.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:45.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:45.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:45.597][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-10-02 19:12:45.601][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:45.602][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:45.605][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-10-02 19:12:45.943][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-10-02 19:12:46.284][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:46.287][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-10-02 19:12:46.293][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-10-02 19:12:46.297][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-10-02 19:12:46.299][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:46.301][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:46.303][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:46.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:46.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:46.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:46.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:46.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:46.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:46.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:46.335][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:46.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:46.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.341][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:46.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:46.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.348][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:46.350][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:46.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.354][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.357][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:46.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:46.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.365][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:46.366][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:46.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.369][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:46.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:46.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.375][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:46.376][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:46.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.379][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:46.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:46.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.387][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:46.388][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:46.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.390][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:46.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:46.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.397][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:46.398][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:46.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.400][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.402][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:46.404][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:46.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.406][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.408][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:46.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:46.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.419][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:46.420][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:46.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.423][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:46.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:46.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.432][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:46.436][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:46.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.439][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:46.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:46.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.445][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:46.445][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:46.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.448][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.450][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:46.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:46.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.455][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:46.456][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:46.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.459][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.461][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:46.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:46.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:46.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:46.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:46.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:46.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:46.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:46.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:46.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:46.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:46.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:46.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:46.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:46.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:46.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:46.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:46.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:46.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:46.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:46.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:46.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:46.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:46.530][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-10-02 19:12:46.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:46.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:46.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:46.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:46.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:46.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:46.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:46.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:46.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:46.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:46.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:46.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:46.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:46.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:46.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:46.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:46.561][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-10-02 19:12:46.562][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:46.564][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-10-02 19:12:46.565][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:46.567][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:46.568][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:46.569][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:46.570][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:46.572][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:46.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:46.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:46.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:46.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:46.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:46.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:46.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:46.595][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-10-02 19:12:46.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:46.601][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:46.603][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-10-02 19:12:46.944][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-10-02 19:12:47.280][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:47.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-10-02 19:12:47.288][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-10-02 19:12:47.291][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-10-02 19:12:47.294][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:47.295][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:47.297][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:47.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:47.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:47.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:47.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:47.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:47.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:47.314][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.TRACE[2024-10-02 19:12:47.316][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:47.317][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:47.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.320][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:47.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:47.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.326][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:47.328][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:47.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.330][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.331][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:47.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:47.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.347][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:47.349][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:47.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.352][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.354][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:47.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:47.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.359][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:47.360][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:47.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.364][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.370][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:47.373][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:47.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.376][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.377][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:47.379][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:47.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.381][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.383][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:47.384][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:47.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.387][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.389][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:47.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:47.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.394][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:47.395][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:47.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.397][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:47.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:47.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.403][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:47.405][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:47.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.407][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:47.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:47.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.414][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:47.415][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:47.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.417][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.419][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:47.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:47.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.424][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:47.425][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:47.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.427][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:47.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:47.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:47.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:47.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:47.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:47.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:47.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:47.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:47.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:47.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:47.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:47.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:47.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:47.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:47.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:47.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:47.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:47.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:47.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:47.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:47.476][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-10-02 19:12:47.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:47.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:47.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:47.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:47.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:47.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:47.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:47.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:47.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:47.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:47.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:47.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:47.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:47.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:47.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:47.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:47.517][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-10-02 19:12:47.519][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:47.521][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-10-02 19:12:47.523][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:47.524][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:47.526][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:47.527][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:47.528][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:47.530][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:47.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:47.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:47.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:47.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:47.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:47.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:47.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:47.551][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-10-02 19:12:47.554][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:47.559][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:47.561][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-10-02 19:12:47.899][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-10-02 19:12:48.236][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:48.239][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-10-02 19:12:48.245][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-10-02 19:12:48.249][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-10-02 19:12:48.252][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:48.254][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:48.256][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:48.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:48.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:48.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:48.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:48.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:48.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:48.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:48.277][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:48.279][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:48.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.282][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:48.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:48.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.289][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:48.290][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:48.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.293][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.295][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:48.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:48.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.300][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:48.302][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:48.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.304][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.305][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:48.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:48.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.310][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:48.311][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:48.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.313][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.314][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:48.316][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:48.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.318][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.320][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:48.321][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:48.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.323][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.324][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:48.325][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:48.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.327][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.329][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:48.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:48.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.345][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:48.347][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:48.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.354][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:48.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:48.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.361][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:48.363][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:48.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.366][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:48.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:48.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.375][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:48.378][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:48.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.380][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:48.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:48.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.387][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:48.388][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:48.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.391][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:48.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:48.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:48.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:48.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:48.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:48.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:48.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:48.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:48.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:48.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:48.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:48.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:48.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:48.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:48.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:48.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:48.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:48.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:48.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:48.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:48.446][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-10-02 19:12:48.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:48.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:48.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:48.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:48.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:48.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:48.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:48.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:48.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:48.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:48.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:48.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:48.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:48.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:48.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:48.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:48.477][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-10-02 19:12:48.478][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:48.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-10-02 19:12:48.481][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:48.483][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:48.484][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:48.485][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:48.487][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:48.487][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:48.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:48.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:48.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:48.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:48.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:48.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:48.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:48.512][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-10-02 19:12:48.515][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:48.517][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:48.518][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-10-02 19:12:48.856][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-10-02 19:12:49.193][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:49.196][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-10-02 19:12:49.201][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-10-02 19:12:49.205][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-10-02 19:12:49.207][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:49.209][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:49.211][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:49.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:49.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:49.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:49.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:49.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:49.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:49.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:49.231][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:49.232][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:49.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.235][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:49.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:49.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.242][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:49.243][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:49.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.246][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.248][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:49.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:49.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.254][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:49.255][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:49.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.258][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.260][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:49.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:49.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.264][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:49.266][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:49.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.268][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:49.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:49.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.276][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:49.278][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:49.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.280][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:49.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:49.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.287][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:49.288][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:49.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.290][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.292][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:49.293][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:49.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.296][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.297][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:49.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:49.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.302][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:49.303][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:49.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.305][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:49.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:49.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.313][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:49.314][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:49.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.317][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.319][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:49.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:49.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.346][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:49.352][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:49.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.357][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.358][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:49.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:49.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.363][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:49.365][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:49.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.367][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.368][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:49.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:49.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:49.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:49.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:49.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:49.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:49.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:49.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:49.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:49.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:49.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:49.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:49.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:49.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:49.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:49.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:49.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:49.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:49.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:49.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:49.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:49.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:49.422][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-10-02 19:12:49.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:49.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:49.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:49.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:49.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:49.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:49.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:49.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:49.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:49.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:49.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:49.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:49.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:49.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:49.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:49.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:49.451][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-10-02 19:12:49.452][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:49.454][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-10-02 19:12:49.455][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:49.456][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:49.458][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:49.459][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:49.461][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:49.462][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:49.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:49.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:49.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:49.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:49.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:49.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:49.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:49.489][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-10-02 19:12:49.492][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:49.494][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:49.503][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-10-02 19:12:49.855][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-10-02 19:12:50.191][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:50.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-10-02 19:12:50.200][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-10-02 19:12:50.204][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-10-02 19:12:50.207][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:50.209][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:50.210][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:50.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:50.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:50.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:50.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:50.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:50.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:50.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:50.228][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:50.230][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:50.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.233][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:50.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:50.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.240][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:50.242][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:50.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.244][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.246][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:50.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:50.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.251][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:50.252][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:50.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.254][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.256][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:50.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:50.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.261][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:50.262][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:50.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.264][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:50.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:50.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.272][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:50.273][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:50.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.275][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:50.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:50.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.282][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:50.283][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:50.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.286][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.287][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:50.288][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:50.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.290][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.292][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:50.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:50.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.297][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:50.299][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:50.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.301][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:50.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:50.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.308][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:50.309][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:50.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.312][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:50.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:50.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.319][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:50.320][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:50.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.322][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.324][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:50.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:50.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.330][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:50.331][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:50.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.343][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.349][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:50.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:50.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:50.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:50.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:50.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:50.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:50.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:50.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:50.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:50.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:50.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:50.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:50.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:50.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:50.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:50.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:50.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:50.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:50.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:50.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:50.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:50.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:50.409][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-10-02 19:12:50.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:50.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:50.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:50.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:50.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:50.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:50.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:50.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:50.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:50.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:50.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:50.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:50.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:50.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:50.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:50.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:50.441][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-10-02 19:12:50.442][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:50.444][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-10-02 19:12:50.446][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:50.447][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:50.449][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:50.450][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:50.451][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:50.453][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:50.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:50.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:50.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:50.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:50.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:50.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:50.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:50.471][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-10-02 19:12:50.475][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:50.476][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:50.478][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-10-02 19:12:50.819][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-10-02 19:12:51.156][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:51.159][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-10-02 19:12:51.164][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-10-02 19:12:51.167][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-10-02 19:12:51.170][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:51.171][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:51.173][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:51.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:51.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:51.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:51.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:51.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:51.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:51.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:51.206][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:51.208][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:51.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.210][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:51.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:51.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.218][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:51.219][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:51.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.222][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.224][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:51.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:51.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.229][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:51.231][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:51.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.233][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.235][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:51.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:51.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.241][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:51.242][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:51.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.245][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:51.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:51.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.252][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:51.253][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:51.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.256][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:51.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:51.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.263][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:51.265][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:51.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.267][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.269][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:51.271][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:51.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.274][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.276][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:51.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:51.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.281][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:51.283][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:51.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.285][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:51.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:51.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.292][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:51.294][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:51.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.296][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.298][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:51.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:51.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.304][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:51.306][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:51.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.308][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.310][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:51.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:51.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.316][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:51.317][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:51.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.319][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.321][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:51.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:51.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:51.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:51.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:51.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:51.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:51.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:51.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:51.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:51.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:51.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:51.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:51.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:51.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:51.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:51.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:51.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:51.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:51.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:51.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:51.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:51.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:51.384][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-10-02 19:12:51.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:51.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:51.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:51.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:51.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:51.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:51.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:51.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:51.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:51.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:51.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:51.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:51.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:51.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:51.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:51.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:51.415][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-10-02 19:12:51.417][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:51.418][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-10-02 19:12:51.420][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:51.422][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:51.423][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:51.425][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:51.426][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:51.428][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:51.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:51.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:51.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:51.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:51.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:51.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:51.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:51.447][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-10-02 19:12:51.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:51.452][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:51.454][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-10-02 19:12:51.797][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-10-02 19:12:52.135][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:52.138][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-10-02 19:12:52.144][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-10-02 19:12:52.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-10-02 19:12:52.152][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:52.154][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:52.155][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:52.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:52.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:52.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:52.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:52.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:52.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:52.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:52.174][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:52.176][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:52.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.179][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:52.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:52.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.200][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:52.202][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:52.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.204][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.205][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:52.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:52.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.210][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:52.211][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:52.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.213][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:52.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:52.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.220][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:52.222][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:52.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:52.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:52.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.232][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:52.233][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:52.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.236][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:52.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:52.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.243][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:52.243][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:52.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.246][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.248][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:52.249][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:52.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.252][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.254][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:52.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:52.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.259][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:52.261][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:52.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.263][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:52.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:52.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.270][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:52.272][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:52.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.274][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:52.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:52.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.281][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:52.282][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:52.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.283][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.285][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:52.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:52.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.289][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:52.291][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:52.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.293][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.295][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:52.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:52.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:52.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:52.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:52.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:52.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:52.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:52.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:52.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:52.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:52.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:52.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:52.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:52.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:52.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:52.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:52.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:52.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:52.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:52.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:52.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:52.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:52.362][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-10-02 19:12:52.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:52.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:52.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:52.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:52.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:52.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:52.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:52.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:52.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:52.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:52.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:52.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:52.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:52.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:52.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:52.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:52.394][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-10-02 19:12:52.395][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:52.397][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-10-02 19:12:52.399][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:52.401][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:52.402][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:52.404][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:52.405][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:52.407][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:52.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:52.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:52.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:52.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:52.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:52.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:52.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:52.426][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-10-02 19:12:52.430][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:52.432][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:52.434][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-10-02 19:12:52.780][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-10-02 19:12:53.116][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-10-02 19:12:53.118][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-10-02 19:12:53.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-10-02 19:12:53.125][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-10-02 19:12:53.129][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-10-02 19:12:53.132][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:53.134][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:53.136][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:53.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:53.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:53.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:53.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:53.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:53.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:53.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:53.157][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:53.159][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:53.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.161][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:53.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:53.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.168][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:53.169][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:53.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.172][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.173][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:53.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:53.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.178][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:53.180][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:53.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.193][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:53.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:53.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.202][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:53.203][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:53.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.206][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.208][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:53.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:53.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.213][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:53.214][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:53.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.217][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:53.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:53.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.224][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:53.225][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:53.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.228][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.229][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:53.231][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:53.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.233][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.235][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:53.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:53.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.241][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:53.242][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:53.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.245][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:53.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:53.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.253][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:53.254][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:53.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.256][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:53.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:53.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.264][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:53.265][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:53.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.268][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.270][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:53.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:53.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.276][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:53.278][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:53.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.280][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.282][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:53.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:53.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:53.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:53.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:53.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:53.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:53.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:53.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:53.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:53.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:53.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:53.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:53.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:53.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:53.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:53.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:53.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:53.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:53.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:53.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:53.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:53.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:53.342][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-10-02 19:12:53.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:53.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:53.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:53.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:53.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:53.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:53.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:53.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:53.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:53.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:53.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:53.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:53.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:53.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:53.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:53.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:53.386][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-10-02 19:12:53.388][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:53.390][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-10-02 19:12:53.392][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:53.394][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:53.395][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:53.397][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:53.398][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:53.399][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:53.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:53.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:53.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:53.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:53.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:53.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:53.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:53.423][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-10-02 19:12:53.427][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:53.428][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:53.431][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-10-02 19:12:53.781][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-10-02 19:12:54.117][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:54.120][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-10-02 19:12:54.125][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-10-02 19:12:54.129][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-10-02 19:12:54.131][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:54.133][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:54.135][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:54.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:54.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:54.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:54.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:54.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:54.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:54.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:54.155][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:54.157][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:54.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.159][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:54.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:54.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.167][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:54.169][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:54.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.171][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.172][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:54.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:54.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.178][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:54.179][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:54.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.181][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:54.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:54.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.188][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:54.189][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:54.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.192][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:54.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:54.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.199][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:54.211][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:54.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.215][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:54.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:54.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.223][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:54.225][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:54.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.227][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.229][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:54.230][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:54.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.232][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.233][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:54.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:54.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.239][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:54.240][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:54.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.243][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:54.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:54.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.251][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:54.252][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:54.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.255][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:54.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:54.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.263][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:54.264][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:54.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.266][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.268][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:54.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:54.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.273][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:54.274][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:54.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.276][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.277][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:54.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:54.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:54.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:54.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:54.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:54.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:54.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:54.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:54.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:54.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:54.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:54.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:54.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:54.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:54.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:54.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:54.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:54.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:54.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:54.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:54.333][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-10-02 19:12:54.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:54.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:54.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:54.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:54.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:54.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:54.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:54.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:54.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:54.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:54.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:54.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:54.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:54.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:54.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:54.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:54.371][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-10-02 19:12:54.373][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:54.375][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-10-02 19:12:54.377][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:54.378][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:54.380][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:54.381][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:54.383][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:54.384][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:54.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:54.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:54.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:54.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:54.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:54.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:54.403][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[2024-10-02 19:12:54.404][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-10-02 19:12:54.408][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:54.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:54.412][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-10-02 19:12:54.772][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-10-02 19:12:55.108][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:55.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-10-02 19:12:55.116][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-10-02 19:12:55.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-10-02 19:12:55.123][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:55.125][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:55.127][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:55.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:55.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:55.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:55.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:55.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:55.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:55.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:55.146][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:55.148][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:55.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.151][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:55.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:55.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.158][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:55.159][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:55.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.161][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.163][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.168][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:55.169][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:55.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.172][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.174][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:55.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:55.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.180][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:55.181][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:55.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.184][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:55.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:55.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.190][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:55.192][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:55.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.194][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:55.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:55.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.202][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:55.203][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:55.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.205][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.206][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:55.207][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:55.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.220][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.222][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:55.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:55.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.228][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:55.230][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:55.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.232][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:55.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:55.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.239][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:55.241][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:55.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.243][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:55.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:55.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.251][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:55.252][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:55.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.254][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.256][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:55.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:55.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.261][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:55.263][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:55.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.265][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.267][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:55.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:55.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:55.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:55.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:55.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:55.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:55.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:55.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:55.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:55.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:55.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:55.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:55.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:55.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:55.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:55.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:55.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:55.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:55.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:55.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:55.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:55.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:55.322][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-10-02 19:12:55.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:55.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:55.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:55.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:55.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:55.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:55.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:55.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:55.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:55.364][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:12:55.376][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:55.377][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:55.380][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:12:55.868][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:12:56.426][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:56.430][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-10-02 19:12:56.435][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-10-02 19:12:56.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:56.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:56.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:56.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:56.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:56.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:56.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:56.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:56.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:56.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:56.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:56.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:57.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:57.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:57.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:57.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:57.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:57.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:57.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:57.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:57.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:57.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:57.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:57.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:57.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:57.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:57.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:57.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:57.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:57.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:57.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:57.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:57.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:57.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:57.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:57.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:57.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:57.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:57.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:57.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:57.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:57.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:57.204][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.INFO [2024-10-02 19:12:57.208][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2024-10-02 19:12:57.210][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:57.211][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:57.214][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:12:57.550][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:12:57.892][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:57.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-10-02 19:12:57.900][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-10-02 19:12:57.904][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:12:57.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:57.910][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:57.912][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:12:58.254][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:12:58.590][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:58.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-10-02 19:12:58.597][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-10-02 19:12:58.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:58.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:58.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:58.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:58.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:58.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:58.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:58.615][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-10-02 19:12:58.616][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:58.618][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-10-02 19:12:58.620][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:58.621][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:58.622][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:58.624][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:58.625][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:58.626][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:58.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:58.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:58.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:58.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:58.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:58.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:58.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:58.645][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-10-02 19:12:58.648][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:58.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:58.651][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-10-02 19:12:58.996][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-10-02 19:12:59.331][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:12:59.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-10-02 19:12:59.336][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-10-02 19:12:59.339][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-10-02 19:12:59.341][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:12:59.342][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:12:59.343][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:12:59.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:59.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:59.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:59.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:59.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:59.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:59.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:59.376][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:59.378][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:59.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.381][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:59.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:59.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.389][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:59.391][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:59.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.394][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.395][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:12:59.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:12:59.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.400][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:59.401][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:59.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.403][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.405][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:12:59.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:12:59.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.410][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:59.411][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:59.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.414][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:12:59.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:12:59.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.421][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:59.422][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:59.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.424][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:12:59.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:12:59.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.431][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:59.432][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:59.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.435][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.436][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:59.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:12:59.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.441][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:59.442][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:59.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.444][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.445][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:12:59.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:12:59.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.450][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.451][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.453][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.459][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:59.460][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:59.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.462][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:12:59.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:12:59.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.468][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:59.469][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:59.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.471][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.473][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:12:59.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:12:59.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.478][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:59.479][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:59.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.481][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.483][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:12:59.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:12:59.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:59.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:59.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:59.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:59.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:59.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:59.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:12:59.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:12:59.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:59.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:59.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:59.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:59.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:59.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:59.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:59.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:59.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:59.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:12:59.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:12:59.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:59.540][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-10-02 19:12:59.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:59.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:59.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:59.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:59.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:59.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:59.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:59.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:12:59.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:12:59.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:12:59.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:12:59.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:12:59.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:59.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:59.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:59.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:59.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:59.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:59.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:12:59.596][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-10-02 19:12:59.597][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:12:59.599][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-10-02 19:12:59.601][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:12:59.603][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:12:59.604][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:12:59.605][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:12:59.606][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:12:59.606][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:12:59.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:12:59.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:12:59.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:12:59.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:12:59.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:12:59.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:12:59.620][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[2024-10-02 19:12:59.621][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-10-02 19:12:59.624][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:12:59.625][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:12:59.626][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-10-02 19:12:59.968][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-10-02 19:13:00.323][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:00.327][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-10-02 19:13:00.331][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-10-02 19:13:00.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-10-02 19:13:00.346][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:13:00.348][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:13:00.350][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:13:00.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:00.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:00.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:00.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:00.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:00.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:00.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:00.369][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:00.370][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:00.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.373][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:00.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:00.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.380][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:00.382][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:00.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.384][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.385][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:00.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.388][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:00.389][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:00.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.391][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.393][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:00.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:00.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.397][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:13:00.398][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:13:00.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.400][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:13:00.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:13:00.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.407][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:13:00.408][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:13:00.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.410][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:13:00.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:13:00.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.416][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:00.417][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:00.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.420][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.421][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:00.422][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:00.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.425][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.426][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:00.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:00.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.431][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.433][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.435][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.442][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:00.443][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:00.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.445][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:00.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:00.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.451][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:00.453][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:00.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.454][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.455][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:00.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:00.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.460][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:00.461][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:00.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.463][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.464][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:00.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:00.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:00.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:00.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:00.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:00.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:00.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:00.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:00.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:00.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:00.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:00.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:00.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:00.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:00.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:00.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:00.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:00.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:00.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:00.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:00.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:00.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:00.526][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-10-02 19:13:00.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:00.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:00.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:00.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:00.568][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:00.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:00.572][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:00.574][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:01.055][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:01.533][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:01.535][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-10-02 19:13:01.540][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-10-02 19:13:01.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:01.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:01.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:01.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:01.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:01.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:01.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:01.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:01.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:01.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:01.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:01.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:01.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:01.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:01.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:01.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:01.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:01.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:01.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:01.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:01.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:01.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:01.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:01.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:01.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:01.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:01.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:01.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:01.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:01.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:01.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:01.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:01.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:01.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:01.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:01.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:01.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:01.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:01.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:01.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:01.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:01.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:01.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:01.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:01.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:01.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:01.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:01.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:01.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:01.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:01.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:01.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:01.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:01.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:01.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:01.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:01.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:01.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:01.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:01.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:01.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:01.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:01.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:01.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:01.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:01.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:01.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:01.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:01.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:01.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:01.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:01.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:01.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:01.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:01.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:02.399][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:02.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 19:13:02.401][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:02.403][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-02 19:13:02.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:02.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:02.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:02.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:02.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:02.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:02.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:02.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:02.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:02.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:02.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:02.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:03.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:03.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:03.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:03.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:03.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:03.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:03.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:03.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:03.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:03.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:03.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.060][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-02 19:13:03.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-02 19:13:03.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 19:13:03.079][biodb::testThat]
biodb.INFO [2024-10-02 19:13:03.081][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-02 19:13:03.082][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:03.084][biodb::testThat]
biodb.TRACE[2024-10-02 19:13:03.090][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-02 19:13:03.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-02 19:13:03.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:03.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:03.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:03.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:03.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:03.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:03.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:03.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:03.133][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:03.138][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:03.139][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:03.141][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:03.479][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:03.813][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:03.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-10-02 19:13:03.823][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-10-02 19:13:03.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:03.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:03.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:03.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:03.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:03.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:03.862][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[2024-10-02 19:13:03.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:03.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:03.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:03.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:03.883][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:03.886][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:03.887][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:03.890][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:04.227][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:04.570][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:04.572][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-10-02 19:13:04.578][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-10-02 19:13:04.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:04.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:04.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:04.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:04.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:04.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:04.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:04.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:04.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:04.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:04.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:04.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:04.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:04.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:04.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:04.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:04.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:04.640][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 19:13:04.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:04.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:04.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:04.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:04.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:04.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:04.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:04.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.663][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.665][private$selectFields]
biodb.TRACE[2024-10-02 19:13:04.666][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:04.667][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:04.668][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.669][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.672][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.673][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.674][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.676][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.678][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.679][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.682][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.684][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.702][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:04.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.731][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-02 19:13:04.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:04.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:04.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:04.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:04.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:04.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:04.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:04.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.754][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.755][private$selectFields]
biodb.TRACE[2024-10-02 19:13:04.756][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:04.758][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:04.759][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.760][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.761][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.763][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.764][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.766][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.768][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.769][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.771][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.772][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.773][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.776][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.777][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:04.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.791][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 19:13:04.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:04.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:04.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:04.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:04.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:04.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:04.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:04.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.814][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.814][private$selectFields]
biodb.TRACE[2024-10-02 19:13:04.815][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:04.816][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:04.817][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.819][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.820][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.822][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.823][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.824][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.826][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.827][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.828][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:04.830][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.831][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.834][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.835][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:04.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:04.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.850][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-02 19:13:04.851][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 19:13:04.853][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 19:13:04.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:04.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:04.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:04.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:04.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:04.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:04.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:04.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:04.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:04.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:04.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:04.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:04.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:04.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:04.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:04.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:04.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:04.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:04.967][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:04.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:04.971][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:04.973][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:05.306][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:05.644][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:05.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-10-02 19:13:05.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-10-02 19:13:05.657][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:05.661][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:05.663][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:05.666][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:06.006][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:06.372][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:06.375][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-10-02 19:13:06.380][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-10-02 19:13:06.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:06.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:06.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:06.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:06.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:06.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:06.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:06.500][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 19:13:06.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:06.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.548][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.549][private$selectFields]
biodb.TRACE[2024-10-02 19:13:06.550][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:06.551][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:06.552][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.553][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.554][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.556][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.558][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.559][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.561][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.562][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.564][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.565][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.566][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.568][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.569][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:06.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.582][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-02 19:13:06.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.593][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.TRACE[2024-10-02 19:13:06.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.634][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.637][private$selectFields]
biodb.TRACE[2024-10-02 19:13:06.639][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:06.640][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:06.642][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.642][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.644][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.646][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.646][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.647][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.649][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.651][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.664][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.665][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.666][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.668][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.669][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:06.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.682][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 19:13:06.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:06.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.706][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.707][private$selectFields]
biodb.TRACE[2024-10-02 19:13:06.708][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:06.709][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:06.711][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.712][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.714][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.716][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.717][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.719][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.721][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.723][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.724][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:06.725][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.726][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.729][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.730][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:06.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.744][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-02 19:13:06.745][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 19:13:06.747][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 19:13:06.758][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-02 19:13:06.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-02 19:13:06.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 19:13:06.770][biodb::testThat]
biodb.INFO [2024-10-02 19:13:06.772][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-02 19:13:06.773][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:06.775][biodb::testThat]
biodb.TRACE[2024-10-02 19:13:06.778][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-02 19:13:06.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-02 19:13:06.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:06.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:06.822][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:06.826][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:06.828][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-02 19:13:06.830][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:06.832][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-02 19:13:06.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:06.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:06.881][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:06.885][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:06.888][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-02 19:13:06.890][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:06.892][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-02 19:13:06.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:06.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:06.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:06.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:06.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:06.968][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 19:13:06.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:06.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:06.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:06.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:06.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:06.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:06.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:06.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:06.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:06.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:06.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.001][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.002][private$selectFields]
biodb.TRACE[2024-10-02 19:13:07.003][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:07.005][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:07.006][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.007][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.009][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.011][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.013][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.015][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.017][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.019][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.020][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.021][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.023][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.026][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.027][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:07.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.046][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-02 19:13:07.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.078][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.080][private$selectFields]
biodb.TRACE[2024-10-02 19:13:07.081][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:07.083][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:07.084][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.091][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.092][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.094][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.096][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.098][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.099][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.101][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.102][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.105][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.106][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:07.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.126][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 19:13:07.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.159][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.161][private$selectFields]
biodb.TRACE[2024-10-02 19:13:07.162][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:07.163][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:07.165][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.168][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.171][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.173][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.175][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.177][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.179][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.180][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.182][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.183][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.185][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.187][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:07.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.206][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-02 19:13:07.207][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 19:13:07.208][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 19:13:07.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:07.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:07.263][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:07.266][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:07.268][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-02 19:13:07.270][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:07.272][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-02 19:13:07.275][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:07.278][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:07.279][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-02 19:13:07.281][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:07.283][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-02 19:13:07.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:07.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:07.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:07.379][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 19:13:07.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.401][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.402][private$selectFields]
biodb.TRACE[2024-10-02 19:13:07.402][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:07.403][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:07.404][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.405][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.407][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.409][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.410][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.412][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.414][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.417][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.422][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.423][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:07.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.438][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-02 19:13:07.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.459][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.460][private$selectFields]
biodb.TRACE[2024-10-02 19:13:07.461][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:07.461][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:07.462][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.463][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.464][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.466][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.467][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.468][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.470][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.471][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.472][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.473][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.475][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.477][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.478][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:07.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.493][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 19:13:07.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.515][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.516][private$selectFields]
biodb.TRACE[2024-10-02 19:13:07.517][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:07.517][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:07.519][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.520][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.522][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.523][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.524][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.526][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.527][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.528][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.530][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.533][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.534][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:07.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.547][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-02 19:13:07.549][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 19:13:07.549][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 19:13:07.561][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-02 19:13:07.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-02 19:13:07.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 19:13:07.572][biodb::testThat]
biodb.INFO [2024-10-02 19:13:07.573][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-02 19:13:07.574][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:07.575][biodb::testThat]
biodb.TRACE[2024-10-02 19:13:07.578][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-02 19:13:07.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-02 19:13:07.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:07.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:07.623][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:07.626][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:07.628][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-02 19:13:07.630][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:07.632][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-02 19:13:07.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:07.666][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:07.669][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:07.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-02 19:13:07.672][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:07.673][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-02 19:13:07.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:07.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:07.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:07.736][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 19:13:07.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.767][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.768][private$selectFields]
biodb.TRACE[2024-10-02 19:13:07.769][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:07.771][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:07.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.773][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.778][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.779][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.780][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.783][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.785][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.786][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.788][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.789][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.800][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.802][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:07.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.819][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-02 19:13:07.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.834][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.TRACE[2024-10-02 19:13:07.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.846][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.847][private$selectFields]
biodb.TRACE[2024-10-02 19:13:07.848][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:07.849][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:07.851][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.852][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.853][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.854][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.855][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.856][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.858][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.859][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.861][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.862][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.863][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.866][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.866][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:07.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.882][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 19:13:07.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:07.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:07.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:07.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:07.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:07.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:07.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:07.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.906][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.907][private$selectFields]
biodb.TRACE[2024-10-02 19:13:07.908][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:07.910][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:07.911][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.914][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.916][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.918][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.919][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.920][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.922][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.923][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:07.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.926][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.929][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.931][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:07.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:07.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.948][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-02 19:13:07.949][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 19:13:07.950][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 19:13:07.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:07.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:07.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:07.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:08.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:08.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:08.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:08.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:08.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:08.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:08.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:08.021][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:08.024][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:08.026][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-02 19:13:08.028][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:08.030][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-02 19:13:08.034][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:08.038][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:08.040][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-02 19:13:08.042][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:08.043][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-02 19:13:08.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:08.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:08.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:08.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:08.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:08.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:08.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:08.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:08.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:08.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:08.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:08.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:08.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:08.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:08.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:08.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:08.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:08.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:08.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:08.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:08.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:08.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:08.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:08.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:08.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:08.126][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 19:13:08.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:08.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:08.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:08.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:08.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:08.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:08.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:08.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.150][private$selectFields]
biodb.TRACE[2024-10-02 19:13:08.151][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:08.152][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:08.152][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.153][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.155][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.157][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.159][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.160][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.163][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.164][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.165][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.169][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.170][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:08.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.187][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-02 19:13:08.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:08.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:08.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:08.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:08.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:08.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:08.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:08.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.214][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.215][private$selectFields]
biodb.TRACE[2024-10-02 19:13:08.216][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:08.217][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:08.219][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.220][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.222][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.223][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.224][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.226][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.227][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.228][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.236][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.238][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.239][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:08.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.251][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 19:13:08.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:08.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:08.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:08.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:08.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:08.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:08.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:08.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.275][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.276][private$selectFields]
biodb.TRACE[2024-10-02 19:13:08.277][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 19:13:08.278][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 19:13:08.279][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.280][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.281][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.283][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.284][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.285][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.287][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.288][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.289][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 19:13:08.291][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.292][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.294][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.296][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 19:13:08.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:08.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:08.311][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-02 19:13:08.312][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 19:13:08.313][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 19:13:08.338][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-02 19:13:08.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-02 19:13:08.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:08.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 19:13:08.346][biodb::testThat]
biodb.INFO [2024-10-02 19:13:08.347][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-10-02 19:13:08.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:08.350][biodb::testThat]
biodb.DEBUG[2024-10-02 19:13:08.352][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-02 19:13:08.353][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:13:08.355][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-10-02 19:13:08.356][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:13:08.357][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:13:08.358][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:13:08.359][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:13:08.360][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:13:08.361][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:13:08.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:08.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:08.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:08.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:08.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:08.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:08.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:08.375][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-10-02 19:13:08.378][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:08.379][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:08.380][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-10-02 19:13:08.718][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-10-02 19:13:09.055][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:09.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-10-02 19:13:09.062][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-10-02 19:13:09.066][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-10-02 19:13:09.068][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:13:09.070][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:13:09.071][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:13:09.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:09.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:09.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:09.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:09.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:09.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:09.088][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[2024-10-02 19:13:09.091][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:09.092][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:09.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.095][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:09.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:09.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.103][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:09.104][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:09.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.107][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.109][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:09.110][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:09.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.113][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.114][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:13:09.115][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:13:09.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.118][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.120][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:13:09.121][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:13:09.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.124][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.126][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:09.127][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:09.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.130][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.131][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:09.133][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:09.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.135][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.137][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:09.139][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:09.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.141][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.143][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:09.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:09.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.147][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.149][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:09.151][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:09.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.154][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.155][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:09.157][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:09.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.159][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:09.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:09.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:09.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:09.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:09.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:09.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:09.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:09.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:09.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:09.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:09.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:09.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:09.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:09.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:09.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:09.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:09.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:09.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:09.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:09.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:09.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:09.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:09.217][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-10-02 19:13:09.218][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-02 19:13:09.232][biodb::testThat]
biodb.INFO [2024-10-02 19:13:09.234][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-02 19:13:09.235][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:09.237][biodb::testThat]
biodb.DEBUG[2024-10-02 19:13:09.253][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-10-02 19:13:09.255][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-10-02 19:13:09.256][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-10-02 19:13:09.259][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-10-02 19:13:09.260][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-10-02 19:13:09.262][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:13:09.263][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:13:09.264][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:13:09.266][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:13:09.267][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:13:09.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:09.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:09.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:09.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:09.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:09.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:09.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:09.287][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-10-02 19:13:09.290][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:09.292][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:09.294][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-10-02 19:13:09.659][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-10-02 19:13:10.149][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:10.152][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-10-02 19:13:10.157][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-10-02 19:13:10.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:10.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:10.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:10.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:10.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:10.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:10.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:10.174][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-10-02 19:13:10.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:10.179][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:10.181][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-10-02 19:13:10.521][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-10-02 19:13:10.867][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:10.869][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-10-02 19:13:10.872][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-10-02 19:13:10.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:10.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:10.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:10.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:10.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:10.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:10.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:10.887][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-10-02 19:13:10.906][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:10.907][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:10.910][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-10-02 19:13:11.245][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-10-02 19:13:11.585][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:11.588][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-10-02 19:13:11.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-10-02 19:13:11.597][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-10-02 19:13:11.601][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:13:11.603][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-10-02 19:13:11.605][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-10-02 19:13:11.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:11.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:11.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:11.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:11.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:11.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:11.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:11.624][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.626][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.628][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.634][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:11.636][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:11.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.638][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.640][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:11.641][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:11.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.643][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.645][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:13:11.646][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:13:11.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.649][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.650][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.652][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.654][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.656][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.657][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.660][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.662][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:11.663][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:11.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.666][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:11.669][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:11.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.671][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.673][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:11.674][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:11.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.676][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.678][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:11.679][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:11.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.682][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.683][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:11.685][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:11.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.687][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:11.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:11.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:11.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:11.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:11.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:11.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:11.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:11.742][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.744][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.746][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.754][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:11.755][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:11.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.758][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.759][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:11.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:11.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.765][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:11.767][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:11.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.770][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:11.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:11.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.777][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:13:11.778][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:13:11.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.781][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:13:11.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:13:11.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.788][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.790][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.792][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.800][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.801][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.804][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.806][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.812][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:11.813][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:11.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.816][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.818][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:11.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:11.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.823][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:11.825][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:11.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.828][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:11.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:11.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.835][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:11.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:11.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.839][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.841][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:11.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:11.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.846][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:11.848][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:11.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.850][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.852][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:11.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:11.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.857][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:11.858][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:11.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.861][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.862][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:11.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:11.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:11.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:11.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:11.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:11.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:11.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:11.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:11.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:11.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:11.920][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.922][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.924][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:11.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:11.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.930][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:11.932][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:11.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.934][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.936][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:11.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:11.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.941][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:11.942][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:11.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.945][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:11.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:11.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.952][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:13:11.953][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:13:11.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.956][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:13:11.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:13:11.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.962][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.963][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.966][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:13:11.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.972][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.974][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.980][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.982][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:11.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.987][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:11.989][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:11.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.991][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.993][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:11.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:11.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:11.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:11.998][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:12.000][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:12.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.002][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:12.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:12.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.009][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:12.010][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:12.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.012][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:12.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:12.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.019][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:12.020][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:12.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.023][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.025][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:12.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:12.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.030][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:12.032][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:12.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.034][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:12.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:12.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:12.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:12.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:12.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:12.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:12.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:12.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:12.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:12.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:12.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:12.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:12.136][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-10-02 19:13:12.137][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-02 19:13:12.139][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-02 19:13:12.160][biodb::testThat]
biodb.INFO [2024-10-02 19:13:12.161][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-10-02 19:13:12.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:12.165][biodb::testThat]
biodb.INFO [2024-10-02 19:13:12.199][biodb::testThat]
biodb.INFO [2024-10-02 19:13:12.201][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-10-02 19:13:12.202][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:12.204][biodb::testThat]
biodb.INFO [2024-10-02 19:13:12.216][biodb::testThat]
biodb.INFO [2024-10-02 19:13:12.218][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-10-02 19:13:12.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:12.220][biodb::testThat]
biodb.DEBUG[2024-10-02 19:13:12.224][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:12.229][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:12.230][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:12.234][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:12.660][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:13.165][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:13.169][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-10-02 19:13:13.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-10-02 19:13:13.194][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:13.196][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:13.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:13.199][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:13.201][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:13.202][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:13.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:13.205][ef$get] fields variable is a list.
biodb.INFO [2024-10-02 19:13:13.207][biodb::testThat]
biodb.INFO [2024-10-02 19:13:13.208][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-02 19:13:13.209][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:13.211][biodb::testThat]
biodb.ERROR[2024-10-02 19:13:13.229][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-02 19:13:13.250][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-02 19:13:13.269][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-02 19:13:13.271][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-02 19:13:13.273][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-02 19:13:13.274][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-02 19:13:13.275][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.278][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.280][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-02 19:13:13.297][biodb::testContext]
biodb.INFO [2024-10-02 19:13:13.299][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 19:13:13.300][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-10-02 19:13:13.301][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 19:13:13.303][biodb::testContext]
biodb.INFO [2024-10-02 19:13:13.306][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-10-02 19:13:13.308][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-02 19:13:13.313][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:13:13.314][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-02 19:13:13.316][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-02 19:13:13.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.320][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-02 19:13:13.321][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-02 19:13:13.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.326][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-02 19:13:13.327][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-02 19:13:13.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.331][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-02 19:13:13.332][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-02 19:13:13.333][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-02 19:13:13.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.336][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[2024-10-02 19:13:13.337][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-02 19:13:13.339][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-02 19:13:13.340][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-02 19:13:13.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.343][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-02 19:13:13.344][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-02 19:13:13.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.347][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-02 19:13:13.348][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-02 19:13:13.349][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-02 19:13:13.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.352][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-02 19:13:13.353][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-02 19:13:13.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.357][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-02 19:13:13.359][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-02 19:13:13.360][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-02 19:13:13.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.365][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-02 19:13:13.366][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-02 19:13:13.368][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-02 19:13:13.369][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-02 19:13:13.370][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-02 19:13:13.372][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-02 19:13:13.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.377][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-02 19:13:13.378][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-02 19:13:13.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.383][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-02 19:13:13.385][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-02 19:13:13.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.390][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-02 19:13:13.391][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-02 19:13:13.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.395][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-02 19:13:13.396][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-02 19:13:13.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.401][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-02 19:13:13.402][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-02 19:13:13.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.407][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-02 19:13:13.408][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-02 19:13:13.432][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-02 19:13:13.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.437][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-02 19:13:13.438][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-02 19:13:13.439][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-02 19:13:13.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.443][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-02 19:13:13.445][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.447][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-02 19:13:13.448][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.449][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:13.451][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.452][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.454][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.455][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.456][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 19:13:13.467][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:13.474][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.475][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-02 19:13:13.477][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:13.478][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.479][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.480][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:13:13.480][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:13:13.480][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:13:13.480][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 19:13:13.480][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 19:13:13.481][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:13.482][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:13.483][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:13.485][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:13.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:13.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:13.488][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.489][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.490][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:13.491][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:13.493][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.494][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.496][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-02 19:13:13.498][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.499][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 19:13:13.501][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.502][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:13.504][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.505][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.506][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.507][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.509][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 19:13:13.510][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:13.511][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.512][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-02 19:13:13.514][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:13.515][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.516][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.518][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:13:13.518][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:13:13.518][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:13:13.518][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 19:13:13.518][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 19:13:13.519][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:13.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:13.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:13.523][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:13.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:13.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:13.527][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.528][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.529][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:13.531][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:13.532][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.533][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.534][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-02 19:13:13.537][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.538][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-02 19:13:13.539][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.541][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:13.542][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.543][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.545][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.546][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.547][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 19:13:13.549][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:13.550][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.551][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-02 19:13:13.553][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:13.554][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.555][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.557][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.558][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:13.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:13.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:13.562][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:13.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:13.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:13.566][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.567][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.569][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:13.570][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:13.571][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.572][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.573][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-02 19:13:13.576][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.577][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 19:13:13.578][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.580][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:13.581][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.582][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.583][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.585][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.586][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 19:13:13.587][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:13.589][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.590][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-02 19:13:13.591][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:13.592][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.593][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.595][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:13.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:13.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:13.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:13.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:13.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:13.604][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.605][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.606][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:13.607][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:13.609][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.610][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:13.612][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:13:13.613][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.619][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[2024-10-02 19:13:13.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.637][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[2024-10-02 19:13:13.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.649][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[2024-10-02 19:13:13.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.715][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-02 19:13:13.716][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-02 19:13:13.718][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-02 19:13:13.719][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-02 19:13:13.721][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 19:13:13.722][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-02 19:13:13.724][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-02 19:13:13.726][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-02 19:13:13.727][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-02 19:13:13.729][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-02 19:13:13.730][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 19:13:13.731][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-02 19:13:13.733][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-02 19:13:13.734][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-02 19:13:13.735][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-02 19:13:13.737][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-02 19:13:13.739][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-02 19:13:13.740][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-02 19:13:13.742][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 19:13:13.744][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-02 19:13:13.745][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-02 19:13:13.746][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-02 19:13:13.748][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-02 19:13:13.750][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-02 19:13:13.751][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-02 19:13:13.753][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-02 19:13:13.754][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-02 19:13:13.756][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-02 19:13:13.758][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-02 19:13:13.759][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-02 19:13:13.761][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-02 19:13:13.763][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-02 19:13:13.765][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-02 19:13:13.766][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-02 19:13:13.768][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-02 19:13:13.770][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-02 19:13:13.771][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-02 19:13:13.773][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-02 19:13:13.774][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-02 19:13:13.776][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-02 19:13:13.777][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-02 19:13:13.779][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-02 19:13:13.780][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-02 19:13:13.782][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-02 19:13:13.783][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-02 19:13:13.785][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-02 19:13:13.786][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-02 19:13:13.788][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-02 19:13:13.789][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-02 19:13:13.791][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-02 19:13:13.793][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-02 19:13:13.794][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-02 19:13:13.796][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-02 19:13:13.798][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-02 19:13:13.799][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-02 19:13:13.801][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-02 19:13:13.803][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-02 19:13:13.804][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-02 19:13:13.805][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-02 19:13:13.806][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-02 19:13:13.808][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-02 19:13:13.809][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-02 19:13:13.810][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-02 19:13:13.811][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-02 19:13:13.813][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-02 19:13:13.814][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-02 19:13:13.815][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 19:13:13.816][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 19:13:13.817][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-02 19:13:13.819][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-02 19:13:13.820][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-02 19:13:13.821][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-02 19:13:13.822][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-02 19:13:13.824][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-02 19:13:13.825][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-02 19:13:13.826][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-02 19:13:13.828][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-02 19:13:13.829][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-02 19:13:13.830][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-02 19:13:13.832][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-02 19:13:13.833][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-02 19:13:13.834][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-02 19:13:13.835][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-02 19:13:13.837][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-02 19:13:13.838][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-10-02 19:13:13.839][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:13:13.840][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.842][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:13.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:13.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:13.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:13.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:13.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:13.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:13.971][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-02 19:13:13.973][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-02 19:13:13.976][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.977][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.979][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.980][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:13.981][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.982][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:13.983][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.984][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-02 19:13:13.985][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-02 19:13:13.987][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:13.988][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:13.989][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-02 19:13:13.990][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-02 19:13:13.992][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-02 19:13:13.993][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:13.994][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:13:13.994][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:13:13.994][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:13:13.996][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-02 19:13:13.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:13.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:13.999][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:14.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:14.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:14.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:14.004][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:13:14.004][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-02 19:13:14.006][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:14.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:14.008][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:14.009][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-02 19:13:14.009][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-02 19:13:14.010][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 19:13:14.012][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 19:13:14.014][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-02 19:13:14.016][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 19:13:14.018][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 19:13:14.020][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 19:13:14.025][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-02 19:13:14.026][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-02 19:13:14.028][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-02 19:13:14.030][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-02 19:13:14.031][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 19:13:14.033][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 19:13:14.035][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-02 19:13:14.037][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-02 19:13:14.039][biodb::testThat]
biodb.INFO [2024-10-02 19:13:14.040][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-10-02 19:13:14.042][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:14.043][biodb::testThat]
biodb.DEBUG[2024-10-02 19:13:14.048][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-02 19:13:14.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:14.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:14.055][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-10-02 19:13:14.385][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-10-02 19:13:14.873][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:14.876][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-10-02 19:13:14.881][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-10-02 19:13:14.885][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:14.890][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:14.891][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:14.893][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:15.236][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:15.572][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:15.576][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-10-02 19:13:15.582][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-10-02 19:13:15.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:15.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:15.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:15.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:15.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:15.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:15.603][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[2024-10-02 19:13:15.606][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:15.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:15.614][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:15.617][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:15.954][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:16.287][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:16.289][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-10-02 19:13:16.294][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-10-02 19:13:16.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:16.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:16.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:16.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:16.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:16.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:16.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:16.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:16.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:16.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:16.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:16.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:16.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:16.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:16.349][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:16.353][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:16.355][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-02 19:13:16.356][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:16.358][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-02 19:13:16.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:16.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:16.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:16.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:16.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:16.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:16.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:16.374][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:16.378][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:16.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-02 19:13:16.382][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:16.384][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-02 19:13:16.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:16.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:16.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:16.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:16.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:16.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:16.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:16.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:16.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:16.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:16.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:16.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:16.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:16.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:16.417][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:16.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:16.423][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-02 19:13:16.424][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:16.426][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-02 19:13:16.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:16.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:16.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:16.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:16.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:16.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:16.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:16.441][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:16.444][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:16.445][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-02 19:13:16.447][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:16.448][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-02 19:13:16.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:16.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:16.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:16.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:16.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:16.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:16.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:16.480][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:16.483][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:16.484][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:16.486][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:16.824][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:17.161][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:17.163][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-10-02 19:13:17.168][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-10-02 19:13:17.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:17.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:17.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:17.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:17.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:17.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:17.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-02 19:13:17.192][biodb::testThat]
biodb.INFO [2024-10-02 19:13:17.193][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-10-02 19:13:17.195][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:17.196][biodb::testThat]
biodb.DEBUG[2024-10-02 19:13:17.201][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:17.204][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:17.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:17.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:17.613][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:17.946][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:17.948][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-10-02 19:13:17.953][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-10-02 19:13:17.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:17.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:17.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:17.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:17.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:17.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:17.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:17.972][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:17.975][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:17.977][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:17.979][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:18.315][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:18.650][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:18.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-10-02 19:13:18.658][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-10-02 19:13:18.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:18.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:18.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:18.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:18.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:18.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.673][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.INFO [2024-10-02 19:13:18.680][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-02 19:13:18.681][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-02 19:13:18.682][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-02 19:13:18.683][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-02 19:13:18.684][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:18.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:18.687][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:18.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:18.689][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-02 19:13:18.695][biodb::testContext]
biodb.INFO [2024-10-02 19:13:18.696][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 19:13:18.697][biodb::testContext] Test context - Test web services
biodb.INFO [2024-10-02 19:13:18.699][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 19:13:18.700][biodb::testContext]
biodb.INFO [2024-10-02 19:13:18.703][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-10-02 19:13:18.706][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-02 19:13:18.711][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:13:18.713][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-02 19:13:18.714][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-02 19:13:18.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.718][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-02 19:13:18.719][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-02 19:13:18.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.724][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-02 19:13:18.725][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-02 19:13:18.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.730][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-02 19:13:18.731][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-02 19:13:18.733][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-02 19:13:18.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.737][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-02 19:13:18.738][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-02 19:13:18.739][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-02 19:13:18.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.743][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-02 19:13:18.744][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-02 19:13:18.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.749][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-02 19:13:18.751][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-02 19:13:18.752][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-02 19:13:18.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.756][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-02 19:13:18.757][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-02 19:13:18.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.761][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[2024-10-02 19:13:18.762][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-02 19:13:18.764][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-02 19:13:18.765][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-02 19:13:18.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.769][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-02 19:13:18.770][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-02 19:13:18.771][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-02 19:13:18.772][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-02 19:13:18.773][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-02 19:13:18.774][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-02 19:13:18.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.778][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-02 19:13:18.779][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-02 19:13:18.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.785][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-02 19:13:18.787][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-02 19:13:18.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.794][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-02 19:13:18.795][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-02 19:13:18.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.800][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-02 19:13:18.802][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-02 19:13:18.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.806][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-02 19:13:18.807][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-02 19:13:18.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.810][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-02 19:13:18.812][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-02 19:13:18.832][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-02 19:13:18.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.838][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-02 19:13:18.839][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-02 19:13:18.841][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-02 19:13:18.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:18.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:18.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:18.846][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-02 19:13:18.849][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.850][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-02 19:13:18.852][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.853][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:18.854][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.856][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.857][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.858][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.859][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 19:13:18.860][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:18.862][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.863][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-02 19:13:18.865][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:18.866][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.867][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.868][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:13:18.868][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:13:18.868][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:13:18.868][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 19:13:18.868][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 19:13:18.869][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:18.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:18.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:18.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:18.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:18.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:18.876][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.877][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.878][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:18.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:18.879][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.881][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.882][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-02 19:13:18.884][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.885][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 19:13:18.886][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.888][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:18.889][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.890][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.891][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.893][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.894][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 19:13:18.896][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:18.897][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.898][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-02 19:13:18.900][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:18.901][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.902][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.904][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:13:18.904][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:13:18.904][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:13:18.904][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 19:13:18.904][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 19:13:18.905][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:18.906][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:18.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:18.909][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:18.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:18.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:18.912][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.914][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.915][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:18.916][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:18.918][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.919][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.921][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-02 19:13:18.923][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.924][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-02 19:13:18.925][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:18.928][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.929][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.930][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.931][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.933][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 19:13:18.934][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:18.936][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.937][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-02 19:13:18.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:18.939][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.940][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.941][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.942][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:18.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:18.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:18.945][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:18.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:18.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:18.948][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.949][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.950][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:18.950][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:18.951][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.952][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.953][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-02 19:13:18.955][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.957][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 19:13:18.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:18.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.962][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.963][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.964][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.965][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 19:13:18.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:18.968][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:18.969][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-02 19:13:18.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:18.972][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.973][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:18.974][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:18.975][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:18.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:18.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:18.984][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:18.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:18.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:18.997][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:18.998][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:19.000][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:19.001][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:19.002][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:19.003][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:19.004][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:13:19.005][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.006][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[2024-10-02 19:13:19.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.036][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[2024-10-02 19:13:19.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.058][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[2024-10-02 19:13:19.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.094][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-02 19:13:19.095][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-02 19:13:19.097][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-02 19:13:19.099][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-02 19:13:19.100][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 19:13:19.102][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-02 19:13:19.104][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-02 19:13:19.106][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-02 19:13:19.107][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-02 19:13:19.108][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-02 19:13:19.110][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 19:13:19.111][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-02 19:13:19.113][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-02 19:13:19.115][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-02 19:13:19.117][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-02 19:13:19.118][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-02 19:13:19.120][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-02 19:13:19.122][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-02 19:13:19.124][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 19:13:19.125][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-02 19:13:19.126][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-02 19:13:19.128][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-02 19:13:19.129][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-02 19:13:19.131][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-02 19:13:19.132][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-02 19:13:19.134][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-02 19:13:19.136][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-02 19:13:19.138][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-02 19:13:19.140][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-02 19:13:19.141][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-02 19:13:19.143][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-02 19:13:19.145][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-02 19:13:19.147][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-02 19:13:19.149][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-02 19:13:19.151][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-02 19:13:19.153][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-02 19:13:19.155][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-02 19:13:19.157][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-02 19:13:19.158][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-02 19:13:19.160][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-02 19:13:19.161][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-02 19:13:19.163][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-02 19:13:19.165][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-02 19:13:19.167][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-02 19:13:19.169][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-02 19:13:19.170][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-02 19:13:19.172][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-02 19:13:19.173][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-02 19:13:19.174][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-02 19:13:19.176][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-02 19:13:19.177][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-02 19:13:19.179][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-02 19:13:19.181][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-02 19:13:19.182][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-02 19:13:19.184][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-02 19:13:19.186][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-02 19:13:19.188][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-02 19:13:19.190][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-02 19:13:19.191][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-02 19:13:19.192][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-02 19:13:19.194][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-02 19:13:19.196][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-02 19:13:19.198][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-02 19:13:19.200][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-02 19:13:19.202][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-02 19:13:19.203][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-02 19:13:19.205][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 19:13:19.207][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 19:13:19.209][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-02 19:13:19.211][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-02 19:13:19.212][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-02 19:13:19.214][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-02 19:13:19.215][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-02 19:13:19.217][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-02 19:13:19.219][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-02 19:13:19.221][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-02 19:13:19.223][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-02 19:13:19.225][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-02 19:13:19.226][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-02 19:13:19.227][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-02 19:13:19.229][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-02 19:13:19.230][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-02 19:13:19.231][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-02 19:13:19.233][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-02 19:13:19.235][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-10-02 19:13:19.236][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:13:19.237][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.240][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.299][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[2024-10-02 19:13:19.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.332][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[2024-10-02 19:13:19.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:19.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:19.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:19.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:19.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:19.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:19.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:19.376][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-02 19:13:19.378][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-02 19:13:19.390][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:19.392][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-02 19:13:19.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:19.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:19.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:19.397][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:19.399][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:19.400][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-02 19:13:19.401][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-02 19:13:19.402][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:19.404][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:19.405][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-02 19:13:19.406][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-02 19:13:19.408][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-02 19:13:19.409][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:19.411][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:13:19.411][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:13:19.411][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:13:19.412][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-02 19:13:19.413][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:19.414][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:19.416][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:19.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:19.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:19.419][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:19.421][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:13:19.421][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-02 19:13:19.422][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:19.423][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:19.424][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:19.425][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-02 19:13:19.425][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-02 19:13:19.427][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 19:13:19.429][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 19:13:19.431][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-02 19:13:19.432][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 19:13:19.434][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 19:13:19.435][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 19:13:19.439][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-02 19:13:19.440][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-02 19:13:19.441][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-02 19:13:19.442][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-02 19:13:19.443][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 19:13:19.444][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 19:13:19.445][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-02 19:13:19.446][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-02 19:13:19.447][biodb::testThat]
biodb.INFO [2024-10-02 19:13:19.448][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-10-02 19:13:19.449][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:19.450][biodb::testThat]
biodb.DEBUG[2024-10-02 19:13:19.452][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-02 19:13:19.455][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:19.457][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-02 19:13:19.458][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:19.459][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-02 19:13:19.462][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:19.465][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:19.466][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:19.467][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-02 19:13:19.806][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-02 19:13:20.139][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:20.142][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-10-02 19:13:20.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-10-02 19:13:20.164][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-02 19:13:20.166][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-02 19:13:20.167][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-02 19:13:20.169][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-02 19:13:20.170][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.173][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.175][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-02 19:13:20.183][biodb::testContext]
biodb.INFO [2024-10-02 19:13:20.184][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 19:13:20.186][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-10-02 19:13:20.187][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 19:13:20.188][biodb::testContext]
biodb.INFO [2024-10-02 19:13:20.191][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-10-02 19:13:20.193][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-02 19:13:20.199][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:13:20.201][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-02 19:13:20.203][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-02 19:13:20.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.207][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.DEBUG[2024-10-02 19:13:20.208][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-02 19:13:20.210][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-02 19:13:20.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.215][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-02 19:13:20.216][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-02 19:13:20.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.221][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-02 19:13:20.223][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-02 19:13:20.224][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-02 19:13:20.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.229][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-02 19:13:20.231][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-02 19:13:20.232][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-02 19:13:20.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.237][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-02 19:13:20.239][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-02 19:13:20.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.243][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-02 19:13:20.245][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-02 19:13:20.246][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-02 19:13:20.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.252][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-02 19:13:20.253][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-02 19:13:20.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.258][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-02 19:13:20.260][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-02 19:13:20.261][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-02 19:13:20.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.266][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-02 19:13:20.268][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-02 19:13:20.269][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-02 19:13:20.271][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-02 19:13:20.272][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-02 19:13:20.274][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-02 19:13:20.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.279][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-02 19:13:20.280][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-02 19:13:20.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.285][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-02 19:13:20.287][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-02 19:13:20.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.292][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-02 19:13:20.293][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-02 19:13:20.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.297][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[2024-10-02 19:13:20.299][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-02 19:13:20.301][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-02 19:13:20.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.306][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-02 19:13:20.308][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-02 19:13:20.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.314][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-02 19:13:20.315][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-02 19:13:20.344][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-02 19:13:20.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.348][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-02 19:13:20.350][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-02 19:13:20.351][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-02 19:13:20.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.355][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.DEBUG[2024-10-02 19:13:20.357][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-02 19:13:20.359][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.361][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-02 19:13:20.362][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.364][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:20.365][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.366][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.368][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.369][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.370][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 19:13:20.372][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:20.373][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.374][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-02 19:13:20.375][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:20.376][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.377][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.378][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:13:20.378][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:13:20.378][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:13:20.378][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 19:13:20.378][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 19:13:20.380][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:20.381][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.382][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.383][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:20.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.386][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.387][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.388][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.390][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:20.391][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:20.392][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.393][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.395][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-02 19:13:20.397][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.399][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 19:13:20.400][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.401][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:20.402][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.404][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.405][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.406][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.408][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 19:13:20.409][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:20.409][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.411][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-02 19:13:20.412][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:20.413][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.414][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.415][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:13:20.415][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:13:20.415][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:13:20.415][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 19:13:20.415][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 19:13:20.416][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:20.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.420][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:20.421][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.422][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.423][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.425][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.426][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:20.427][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:20.429][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.430][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.431][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-02 19:13:20.434][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.435][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-02 19:13:20.437][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.438][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:20.439][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.440][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.442][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.443][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.444][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 19:13:20.446][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:20.448][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.449][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-02 19:13:20.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:20.451][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.452][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.454][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.455][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:20.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.459][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:20.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.462][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.463][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.464][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:20.465][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:20.467][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.468][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.469][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-02 19:13:20.471][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.473][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 19:13:20.474][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.475][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:20.476][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.477][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.478][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.479][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.480][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 19:13:20.481][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:20.482][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.484][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-02 19:13:20.485][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:20.486][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.488][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.489][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.491][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 19:13:20.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.494][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:20.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.498][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.499][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.500][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:20.502][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:20.503][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.504][self$setPropertyValue]
biodb.DEBUG[2024-10-02 19:13:20.506][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:13:20.507][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.577][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[2024-10-02 19:13:20.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.584][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[2024-10-02 19:13:20.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.603][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[2024-10-02 19:13:20.603][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-02 19:13:20.605][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-02 19:13:20.607][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-02 19:13:20.608][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-02 19:13:20.610][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 19:13:20.611][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-02 19:13:20.612][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-02 19:13:20.614][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-02 19:13:20.616][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-02 19:13:20.617][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-02 19:13:20.618][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 19:13:20.619][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-02 19:13:20.621][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-02 19:13:20.622][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-02 19:13:20.623][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-02 19:13:20.625][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-02 19:13:20.626][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-02 19:13:20.628][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-02 19:13:20.629][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 19:13:20.630][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-02 19:13:20.631][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-02 19:13:20.633][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-02 19:13:20.634][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-02 19:13:20.635][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-02 19:13:20.637][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-02 19:13:20.638][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-02 19:13:20.639][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-02 19:13:20.641][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-02 19:13:20.642][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-02 19:13:20.644][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-02 19:13:20.645][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-02 19:13:20.647][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-02 19:13:20.648][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-02 19:13:20.650][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-02 19:13:20.651][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-02 19:13:20.652][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-02 19:13:20.654][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-02 19:13:20.655][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-02 19:13:20.657][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-02 19:13:20.658][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-02 19:13:20.660][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-02 19:13:20.662][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-02 19:13:20.664][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-02 19:13:20.666][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-02 19:13:20.667][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-02 19:13:20.669][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-02 19:13:20.671][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-02 19:13:20.673][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-02 19:13:20.675][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-02 19:13:20.676][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-02 19:13:20.678][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-02 19:13:20.680][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-02 19:13:20.681][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-02 19:13:20.682][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-02 19:13:20.684][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-02 19:13:20.685][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-02 19:13:20.686][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-02 19:13:20.688][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-02 19:13:20.689][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-02 19:13:20.691][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-02 19:13:20.692][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-02 19:13:20.693][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-02 19:13:20.695][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-02 19:13:20.696][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-02 19:13:20.697][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-02 19:13:20.699][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-02 19:13:20.701][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 19:13:20.703][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 19:13:20.705][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-02 19:13:20.707][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-02 19:13:20.708][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-02 19:13:20.710][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-02 19:13:20.712][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-02 19:13:20.713][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-02 19:13:20.714][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-02 19:13:20.716][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-02 19:13:20.718][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-02 19:13:20.719][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-02 19:13:20.721][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-02 19:13:20.722][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-02 19:13:20.723][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-02 19:13:20.725][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-02 19:13:20.726][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-02 19:13:20.727][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-02 19:13:20.729][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-10-02 19:13:20.731][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 19:13:20.732][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.734][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.754][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[2024-10-02 19:13:20.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.761][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[2024-10-02 19:13:20.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.780][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[2024-10-02 19:13:20.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 19:13:20.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.853][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-02 19:13:20.855][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-02 19:13:20.857][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.859][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.860][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.861][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 19:13:20.862][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.863][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.865][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.865][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-02 19:13:20.866][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-02 19:13:20.867][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 19:13:20.868][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.869][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-02 19:13:20.878][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-02 19:13:20.879][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-02 19:13:20.881][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-02 19:13:20.883][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 19:13:20.883][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 19:13:20.883][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 19:13:20.884][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-02 19:13:20.885][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.886][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.888][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 19:13:20.889][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 19:13:20.890][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 19:13:20.890][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 19:13:20.891][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:13:20.891][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-02 19:13:20.892][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 19:13:20.893][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 19:13:20.894][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-02 19:13:20.895][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-02 19:13:20.895][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-02 19:13:20.896][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 19:13:20.897][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 19:13:20.899][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-02 19:13:20.901][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 19:13:20.903][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 19:13:20.905][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 19:13:20.908][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-02 19:13:20.910][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-02 19:13:20.911][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-02 19:13:20.913][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-02 19:13:20.914][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 19:13:20.915][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 19:13:20.917][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-02 19:13:20.918][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-02 19:13:20.919][biodb::testThat]
biodb.INFO [2024-10-02 19:13:20.920][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-10-02 19:13:20.921][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 19:13:20.922][biodb::testThat]
biodb.DEBUG[2024-10-02 19:13:20.925][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-02 19:13:20.930][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:20.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-02 19:13:20.934][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:20.936][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-02 19:13:20.941][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 19:13:20.944][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 19:13:20.946][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-10-02 19:13:20.947][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 19:13:20.949][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-10-02 19:13:20.953][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-10-02 19:13:20.955][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 19:13:20.957][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-10-02 19:13:20.959][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 19:13:20.960][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 19:13:20.961][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 19:13:20.962][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 19:13:20.963][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 19:13:20.965][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 19:13:20.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:20.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:20.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:20.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:20.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:20.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:20.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 19:13:20.982][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-10-02 19:13:20.986][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 19:13:20.987][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 19:13:20.989][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-10-02 19:13:21.756][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-10-02 19:13:22.807][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 19:13:22.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-10-02 19:13:22.815][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-10-02 19:13:22.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-10-02 19:13:22.820][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 19:13:22.821][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 19:13:22.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 19:13:22.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 19:13:22.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:22.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:22.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:22.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:22.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:22.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 19:13:22.842][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:22.843][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:22.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.846][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:22.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:22.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.853][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:22.854][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:22.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.856][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 19:13:22.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 19:13:22.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.862][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:22.863][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:22.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.865][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.866][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 19:13:22.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 19:13:22.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.870][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 19:13:22.871][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 19:13:22.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.873][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.874][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 19:13:22.875][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 19:13:22.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.877][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.879][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:22.880][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:22.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.882][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.884][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:22.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 19:13:22.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.889][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:22.891][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:22.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.893][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.895][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 19:13:22.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 19:13:22.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.900][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:22.901][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:22.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.903][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:22.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 19:13:22.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.908][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:22.909][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:22.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.911][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.913][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 19:13:22.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 19:13:22.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.917][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:22.918][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:22.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.919][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.921][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 19:13:22.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 19:13:22.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.926][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:22.927][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:22.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.929][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.931][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 19:13:22.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 19:13:22.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:22.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:22.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:22.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:22.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:22.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:22.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 19:13:22.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 19:13:22.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:22.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:22.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:22.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:22.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:22.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:22.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:22.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:22.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:22.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:22.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 19:13:22.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 19:13:22.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 19:13:22.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 19:13:22.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 19:13:22.976][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-10-02 19:13:22.983][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-02 19:13:22.984][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-02 19:13:22.985][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-02 19:13:22.987][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-02 19:13:22.987][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 19:13:22.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 19:13:22.989][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 19:13:22.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 19:13:22.991][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 19:13:22.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 22.399   1.414  58.726

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	3.085	1.232	8.546
ChebiEntry	0.497	0.019	0.574