Multiple platform build/check report for BioC 3.20 - CHECK results for biodbChebi on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4358
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 nebbiolo2

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: 1.12.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.12.0.tar.gz

StartedAt: 2025-01-02 20:18:22 -0500 (Thu, 02 Jan 2025)

EndedAt: 2025-01-02 20:20:21 -0500 (Thu, 02 Jan 2025)

EllapsedTime: 119.1 seconds

RetCode: 0

Status: OK

CheckDir: biodbChebi.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 [2025-01-02 20:19:05.415][biodb::testContext]
biodb.INFO [2025-01-02 20:19:05.417][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-02 20:19:05.418][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-01-02 20:19:05.419][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-02 20:19:05.420][biodb::testContext]
biodb.INFO [2025-01-02 20:19:05.427][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-02 20:19:05.429][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-02 20:19:05.437][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:05.438][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-02 20:19:05.439][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-02 20:19:05.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.443][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-02 20:19:05.464][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-02 20:19:05.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.468][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-02 20:19:05.469][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-02 20:19:05.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.473][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-02 20:19:05.474][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-02 20:19:05.475][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-02 20:19:05.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.478][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[2025-01-02 20:19:05.479][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-02 20:19:05.480][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-02 20:19:05.481][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-02 20:19:05.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.485][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-02 20:19:05.486][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-02 20:19:05.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.490][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-02 20:19:05.491][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-02 20:19:05.492][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-02 20:19:05.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.496][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-02 20:19:05.497][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-02 20:19:05.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.501][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-02 20:19:05.502][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-02 20:19:05.503][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-02 20:19:05.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.506][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-02 20:19:05.508][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-02 20:19:05.509][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-02 20:19:05.510][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-02 20:19:05.511][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-02 20:19:05.512][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-02 20:19:05.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.515][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[2025-01-02 20:19:05.516][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-02 20:19:05.517][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-02 20:19:05.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.521][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-02 20:19:05.522][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-02 20:19:05.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.526][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-02 20:19:05.527][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-02 20:19:05.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.530][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-02 20:19:05.532][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-02 20:19:05.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.535][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-02 20:19:05.537][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-02 20:19:05.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.541][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-02 20:19:05.542][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-02 20:19:05.546][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-02 20:19:05.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.549][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-02 20:19:05.550][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-02 20:19:05.552][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-02 20:19:05.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.558][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-02 20:19:05.595][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.613][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-02 20:19:05.615][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.616][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:05.617][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.618][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.626][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.627][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.628][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-02 20:19:05.629][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:05.630][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.631][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-02 20:19:05.632][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:05.633][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.633][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.634][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:05.634][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:05.634][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:05.634][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-02 20:19:05.634][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-02 20:19:05.635][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:05.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:05.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:05.638][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:05.639][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:05.640][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:05.641][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.642][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.642][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:05.643][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:05.644][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.645][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.646][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-02 20:19:05.648][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.649][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-02 20:19:05.649][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.650][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:05.651][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.652][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.653][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.654][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.655][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-02 20:19:05.656][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:05.657][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.658][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-02 20:19:05.659][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:05.660][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.660][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.661][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:05.661][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:05.661][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:05.661][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-02 20:19:05.661][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-02 20:19:05.662][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:05.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:05.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:05.665][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:05.666][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:05.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:05.675][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.677][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.678][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:05.679][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:05.680][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.681][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.682][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-02 20:19:05.684][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.685][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-02 20:19:05.686][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.687][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:05.688][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.689][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.690][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.691][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.692][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-02 20:19:05.693][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:05.694][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.695][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-02 20:19:05.696][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:05.697][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.698][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.699][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.700][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:05.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:05.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:05.703][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:05.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:05.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:05.706][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.707][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.708][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:05.709][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:05.710][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.711][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.712][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-02 20:19:05.714][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.715][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-02 20:19:05.716][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.717][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:05.718][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.719][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.720][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.722][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.723][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-02 20:19:05.724][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:05.725][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.726][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-02 20:19:05.727][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:05.728][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.729][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:05.730][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.731][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:05.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:05.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:05.734][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:05.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:05.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:05.737][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:05.738][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.739][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:05.740][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:05.741][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:05.742][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:05.746][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:05.747][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.748][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[2025-01-02 20:19:05.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.771][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[2025-01-02 20:19:05.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.780][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[2025-01-02 20:19:05.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.798][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[2025-01-02 20:19:05.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.803][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[2025-01-02 20:19:05.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.826][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-02 20:19:05.831][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-02 20:19:05.833][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-02 20:19:05.834][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-02 20:19:05.836][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-02 20:19:05.837][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-02 20:19:05.838][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-02 20:19:05.840][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-02 20:19:05.841][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-02 20:19:05.843][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-02 20:19:05.844][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-02 20:19:05.846][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-02 20:19:05.847][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-02 20:19:05.848][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-02 20:19:05.850][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-02 20:19:05.851][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-02 20:19:05.853][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-02 20:19:05.854][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-02 20:19:05.855][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-02 20:19:05.857][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-02 20:19:05.858][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-02 20:19:05.860][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-02 20:19:05.861][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-02 20:19:05.863][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-02 20:19:05.864][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-02 20:19:05.866][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-02 20:19:05.867][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-02 20:19:05.868][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-02 20:19:05.870][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-02 20:19:05.871][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-02 20:19:05.873][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-02 20:19:05.874][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-02 20:19:05.876][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-02 20:19:05.877][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-02 20:19:05.878][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-02 20:19:05.880][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-02 20:19:05.881][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-02 20:19:05.882][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-02 20:19:05.884][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-02 20:19:05.885][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-02 20:19:05.887][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-02 20:19:05.888][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-02 20:19:05.889][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-02 20:19:05.891][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-02 20:19:05.892][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-02 20:19:05.894][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-02 20:19:05.895][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-02 20:19:05.897][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-02 20:19:05.898][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-02 20:19:05.912][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-02 20:19:05.913][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-02 20:19:05.915][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-02 20:19:05.916][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-02 20:19:05.918][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-02 20:19:05.919][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-02 20:19:05.920][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-02 20:19:05.922][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-02 20:19:05.923][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-02 20:19:05.925][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-02 20:19:05.926][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-02 20:19:05.928][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-02 20:19:05.929][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-02 20:19:05.930][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-02 20:19:05.932][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-02 20:19:05.933][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-02 20:19:05.935][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-02 20:19:05.936][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-02 20:19:05.938][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-02 20:19:05.939][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-02 20:19:05.941][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-02 20:19:05.942][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-02 20:19:05.944][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-02 20:19:05.945][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-02 20:19:05.947][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-02 20:19:05.948][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-02 20:19:05.949][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-02 20:19:05.951][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-02 20:19:05.952][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-02 20:19:05.954][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-02 20:19:05.955][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-02 20:19:05.956][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-02 20:19:05.958][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-02 20:19:05.959][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-02 20:19:05.965][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-02 20:19:05.966][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-02 20:19:05.969][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:05.970][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.972][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:05.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:05.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:05.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:05.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:05.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:05.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:05.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:05.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:05.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:05.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:05.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:05.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:05.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:06.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:06.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.011][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[2025-01-02 20:19:06.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.017][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[2025-01-02 20:19:06.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.022][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[2025-01-02 20:19:06.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.028][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[2025-01-02 20:19:06.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:06.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:06.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:06.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:06.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:06.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.062][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[2025-01-02 20:19:06.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.068][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[2025-01-02 20:19:06.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:06.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:06.075][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-02 20:19:06.085][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-02 20:19:06.087][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:06.088][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-02 20:19:06.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:06.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:06.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:06.092][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:06.093][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:06.094][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-02 20:19:06.095][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-02 20:19:06.096][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:06.097][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:06.098][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-02 20:19:06.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-02 20:19:06.100][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-02 20:19:06.101][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:06.102][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:06.102][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:06.102][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:06.103][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-02 20:19:06.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:06.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:06.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:06.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:06.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:06.108][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:06.109][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:06.109][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-02 20:19:06.110][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:06.110][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:06.111][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:06.112][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-02 20:19:06.112][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-02 20:19:06.118][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-02 20:19:06.120][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-02 20:19:06.121][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-02 20:19:06.122][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-02 20:19:06.124][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-02 20:19:06.125][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-02 20:19:06.147][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-02 20:19:06.149][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-02 20:19:06.153][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-02 20:19:06.156][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-02 20:19:06.160][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-02 20:19:06.161][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-02 20:19:06.163][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-02 20:19:06.164][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-02 20:19:06.179][biodb::testThat]
biodb.INFO [2025-01-02 20:19:06.180][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-02 20:19:06.181][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:06.182][biodb::testThat]
biodb.TRACE[2025-01-02 20:19:06.185][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-01-02 20:19:06.187][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:06.190][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:06.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:06.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:06.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:06.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:06.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:06.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:06.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:06.221][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.222][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.224][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.241][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:06.242][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:06.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.243][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.269][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:06.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:06.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.273][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:06.274][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:06.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.275][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:06.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:06.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.280][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.281][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.283][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.288][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.289][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.291][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.296][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.297][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.299][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.300][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.304][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:06.305][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.307][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.308][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:06.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.312][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.313][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.315][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.320][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:06.321][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:06.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.323][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.324][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:06.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:06.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.328][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:06.329][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.331][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.332][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:06.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.336][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:06.337][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:06.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.339][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.340][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:06.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:06.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:06.419][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-01-02 20:19:06.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.465][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-02 20:19:06.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-02 20:19:06.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.469][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-02 20:19:06.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-02 20:19:06.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.473][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-02 20:19:06.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-02 20:19:06.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.477][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-02 20:19:06.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-02 20:19:06.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.572][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.573][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.575][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.598][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.599][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.601][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:06.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:06.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:06.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:06.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:06.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:06.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:06.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.649][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:06.650][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:06.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.652][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:06.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.664][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:06.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:06.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.668][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:06.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:06.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.672][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:06.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:06.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.675][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:06.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:06.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.678][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.679][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:06.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:06.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.701][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.702][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.704][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.728][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.731][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.743][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:06.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:06.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.747][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:06.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:06.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.751][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:06.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:06.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.754][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:06.755][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:06.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.757][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.758][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:06.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:06.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.769][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.773][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.776][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.780][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.781][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.783][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.784][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.795][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.799][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.802][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.806][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.807][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.809][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.810][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.821][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:06.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:06.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.824][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:06.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:06.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.828][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:06.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:06.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.832][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:06.833][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:06.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.835][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.836][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:06.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:06.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.858][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.859][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.861][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.889][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.890][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.892][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.903][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:06.904][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:06.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.906][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.910][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:06.911][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:06.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.913][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.917][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:06.918][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:06.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.920][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.924][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:06.925][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:06.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.926][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.931][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.932][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:06.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.933][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.937][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.938][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:06.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.940][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.944][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.945][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:06.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.947][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.951][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.952][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:06.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.954][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.958][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.959][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:06.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.960][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.964][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:06.965][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:06.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.967][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:06.971][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:06.972][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:06.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:06.974][ef$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:06.981][biodb::testThat]
biodb.INFO [2025-01-02 20:19:06.982][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-02 20:19:06.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:06.983][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:06.996][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-01-02 20:19:07.003][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:07.008][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-01-02 20:19:07.009][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:07.010][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-01-02 20:19:07.011][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:07.034][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:07.035][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:07.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:07.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:07.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:07.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:07.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:07.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:07.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:07.048][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:07.049][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:07.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.050][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:07.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:07.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.071][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:07.077][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:07.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.079][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.080][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:07.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:07.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.084][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:07.085][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:07.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.087][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:07.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:07.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.092][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:07.093][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:07.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.094][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:07.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:07.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.099][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:07.100][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:07.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.102][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.103][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:07.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:07.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.107][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:07.108][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:07.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.110][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.111][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:07.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:07.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.115][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:07.116][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:07.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.117][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.119][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:07.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:07.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.122][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:07.123][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:07.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.125][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:07.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:07.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.130][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:07.131][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:07.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.132][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.134][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:07.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:07.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.137][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:07.138][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:07.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.140][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.141][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:07.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:07.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.145][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:07.146][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:07.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.148][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.149][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:07.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:07.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:07.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:07.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:07.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:07.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:07.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:07.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:07.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:07.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:07.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:07.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:07.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:07.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:07.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:07.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:07.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:07.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:07.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:07.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:07.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:07.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:07.188][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-01-02 20:19:07.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-02 20:19:07.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-02 20:19:07.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-02 20:19:07.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-02 20:19:07.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-02 20:19:07.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-02 20:19:07.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:07.206][biodb::testThat]
biodb.INFO [2025-01-02 20:19:07.207][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-02 20:19:07.208][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:07.209][biodb::testThat]
biodb.TRACE[2025-01-02 20:19:07.212][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:07.213][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:07.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.215][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:07.216][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-01-02 20:19:07.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:07.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:07.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.243][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:07.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:07.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:07.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:07.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:07.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:07.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:07.252][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-01-02 20:19:07.256][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-02 20:19:07.276][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:07.296][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-02 20:19:07.297][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:07.298][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-02 20:19:07.320][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[2025-01-02 20:19:07.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:07.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:07.325][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-02 20:19:07.953][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:08.475][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:08.478][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-01-02 20:19:08.492][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-01-02 20:19:08.495][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-01-02 20:19:08.505][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:08.507][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:08.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.508][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.509][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.510][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.512][ef$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:08.516][biodb::testThat]
biodb.INFO [2025-01-02 20:19:08.516][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-02 20:19:08.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:08.518][biodb::testThat]
biodb.TRACE[2025-01-02 20:19:08.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:08.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:08.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:08.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:08.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:08.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:08.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:08.612][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:08.615][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:08.616][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-02 20:19:08.617][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:08.618][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-01-02 20:19:08.632][biodb::testThat]
biodb.INFO [2025-01-02 20:19:08.633][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-02 20:19:08.633][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:08.634][biodb::testThat]
biodb.TRACE[2025-01-02 20:19:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:08.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:08.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:08.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:08.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:08.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:08.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:08.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:08.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.674][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-02 20:19:08.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-02 20:19:08.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.677][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-02 20:19:08.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-02 20:19:08.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.681][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-02 20:19:08.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-02 20:19:08.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.685][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-02 20:19:08.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-02 20:19:08.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:08.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:08.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:08.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:08.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:08.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:08.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:08.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:08.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:08.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.731][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-02 20:19:08.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-02 20:19:08.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.735][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-02 20:19:08.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-02 20:19:08.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.739][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-02 20:19:08.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-02 20:19:08.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:08.742][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-02 20:19:08.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-02 20:19:08.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:08.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:08.751][biodb::testThat]
biodb.INFO [2025-01-02 20:19:08.752][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-02 20:19:08.753][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:08.753][biodb::testThat]
biodb.INFO [2025-01-02 20:19:08.761][biodb::testThat]
biodb.INFO [2025-01-02 20:19:08.761][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-02 20:19:08.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:08.763][biodb::testThat]
biodb.INFO [2025-01-02 20:19:08.770][biodb::testThat]
biodb.INFO [2025-01-02 20:19:08.771][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-02 20:19:08.772][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:08.773][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:08.776][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-01-02 20:19:09.563][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-01-02 20:19:10.955][biodb::testThat]
biodb.INFO [2025-01-02 20:19:10.958][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-02 20:19:10.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:10.961][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:11.620][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[2025-01-02 20:19:12.036][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:12.037][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:12.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.040][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:12.041][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:12.042][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:12.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.044][ef$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:12.046][biodb::testThat]
biodb.INFO [2025-01-02 20:19:12.047][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-01-02 20:19:12.048][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:12.049][biodb::testThat]
biodb.TRACE[2025-01-02 20:19:12.061][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:12.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:12.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:12.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:12.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:12.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:12.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:12.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:12.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:12.175][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:12.179][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:12.180][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-02 20:19:12.182][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:12.183][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-02 20:19:12.246][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:12.249][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:12.251][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-02 20:19:12.252][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:12.253][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-01-02 20:19:12.267][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-02 20:19:12.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-02 20:19:12.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:12.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:12.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:12.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:12.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:12.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:12.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:12.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:12.299][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:12.314][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:12.315][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:12.336][private$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[2025-01-02 20:19:12.677][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[2025-01-02 20:19:13.023][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:13.029][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-01-02 20:19:13.038][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-01-02 20:19:13.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:13.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:13.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:13.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:13.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:13.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:13.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:13.069][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-01-02 20:19:13.142][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:13.144][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-01-02 20:19:13.146][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:13.147][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:13.148][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:13.149][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:13.151][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:13.151][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:13.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:13.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:13.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:13.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:13.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:13.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:13.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:13.165][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-01-02 20:19:13.168][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:13.169][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:13.170][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-01-02 20:19:13.508][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-01-02 20:19:13.859][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:13.862][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-01-02 20:19:13.866][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-01-02 20:19:13.869][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-01-02 20:19:13.870][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:13.872][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:13.873][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:13.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:13.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:13.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:13.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:13.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:13.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:13.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:13.888][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:13.889][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:13.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.891][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:13.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:13.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.897][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:13.898][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:13.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.900][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.901][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:13.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:13.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.905][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:13.907][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:13.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.909][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.910][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:13.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:13.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.915][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:13.916][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:13.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.917][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:13.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:13.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.937][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:13.939][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:13.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.940][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:13.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:13.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.947][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:13.948][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:13.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.950][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.951][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:13.952][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:13.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.954][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.955][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:13.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:13.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.959][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:13.960][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:13.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.962][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:13.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:13.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.967][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:13.968][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:13.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.970][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:13.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.976][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:13.977][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:13.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.978][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.980][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:13.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:13.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:13.984][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:13.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.986][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.987][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:13.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:13.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:13.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:13.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:13.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:13.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:13.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:13.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:14.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:14.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:14.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:14.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:14.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:14.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:14.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:14.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:14.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:14.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:14.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:14.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:14.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:14.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:14.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:14.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:14.029][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-01-02 20:19:14.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:14.051][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[2025-01-02 20:19:14.054][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:14.055][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:14.057][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-02 20:19:14.403][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:14.761][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:14.775][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-01-02 20:19:14.788][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-01-02 20:19:14.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:14.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:14.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:14.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:14.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:14.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:14.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:14.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:14.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:14.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:14.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:14.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:14.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:14.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:14.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:14.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:14.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:14.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:14.929][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-01-02 20:19:14.930][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:14.933][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-01-02 20:19:14.935][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:14.936][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:14.938][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:14.939][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:14.941][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:14.943][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:14.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:14.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:14.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:14.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:14.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:14.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:14.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:14.977][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-01-02 20:19:14.980][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:14.981][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:14.983][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-01-02 20:19:15.325][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-01-02 20:19:15.678][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:15.684][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-01-02 20:19:15.693][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-01-02 20:19:15.701][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-01-02 20:19:15.705][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:15.709][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:15.712][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:15.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:15.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:15.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:15.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:15.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:15.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:15.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:15.739][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:15.741][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:15.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.744][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:15.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:15.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.752][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:15.753][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:15.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.756][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.758][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:15.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:15.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.762][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:15.763][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:15.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.765][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:15.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:15.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.772][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:15.773][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:15.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.775][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:15.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:15.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.782][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:15.783][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:15.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.786][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:15.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:15.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.792][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:15.793][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:15.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.796][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.797][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:15.799][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.801][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.803][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:15.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.808][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:15.809][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:15.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.811][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:15.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:15.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.816][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:15.817][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:15.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.819][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:15.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:15.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.824][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:15.825][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:15.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.826][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.828][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:15.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:15.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.831][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:15.832][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:15.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.834][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.835][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:15.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:15.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:15.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:15.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:15.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:15.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:15.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:15.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:15.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:15.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:15.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:15.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:15.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:15.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:15.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:15.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:15.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:15.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:15.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:15.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:15.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:15.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:15.884][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-01-02 20:19:15.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:15.913][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:15.916][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:15.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-02 20:19:15.919][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:15.920][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-02 20:19:15.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:15.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:15.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:15.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:15.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:15.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:15.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:15.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:15.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:15.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:15.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:15.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:15.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:15.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:15.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:15.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:15.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:15.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:15.953][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-01-02 20:19:15.954][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:15.955][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-01-02 20:19:15.956][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:15.957][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:15.958][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:15.959][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:15.960][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:15.961][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:15.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:15.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:15.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:15.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:15.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:15.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:15.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:15.973][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-01-02 20:19:15.976][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:15.977][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:15.978][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-01-02 20:19:16.324][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-01-02 20:19:16.675][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:16.680][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-01-02 20:19:16.686][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-01-02 20:19:16.691][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-01-02 20:19:16.694][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:16.697][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:16.699][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:16.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:16.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:16.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:16.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:16.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:16.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:16.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:16.723][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:16.725][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:16.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.728][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:16.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:16.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.736][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:16.737][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:16.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.740][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.741][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:16.743][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:16.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.745][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.747][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:16.748][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:16.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.750][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.751][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:16.752][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:16.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.755][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.756][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:16.757][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:16.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.759][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.760][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:16.761][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.763][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.765][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:16.775][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:16.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.777][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.778][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:16.779][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:16.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.781][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:16.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:16.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.786][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:16.787][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:16.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.789][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.790][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:16.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:16.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.794][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:16.795][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:16.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.797][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:16.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:16.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:16.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:16.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:16.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:16.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:16.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:16.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:16.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:16.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:16.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:16.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:16.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:16.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:16.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:16.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:16.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:16.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:16.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:16.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:16.836][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-01-02 20:19:16.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:16.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:16.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:16.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:16.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:16.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:16.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:16.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:16.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:16.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:16.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:16.866][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-01-02 20:19:16.867][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:16.868][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-01-02 20:19:16.870][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:16.871][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:16.872][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:16.873][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:16.874][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:16.875][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:16.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:16.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:16.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:16.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:16.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:16.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:16.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:16.887][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-01-02 20:19:16.890][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:16.891][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:16.892][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-01-02 20:19:17.241][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-01-02 20:19:17.594][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:17.598][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-01-02 20:19:17.605][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-01-02 20:19:17.611][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-01-02 20:19:17.614][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:17.617][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:17.619][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:17.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:17.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:17.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:17.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:17.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:17.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:17.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:17.645][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:17.647][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:17.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.650][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:17.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:17.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.657][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:17.659][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:17.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.661][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.663][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:17.664][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:17.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.666][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.668][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:17.669][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:17.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.671][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.673][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:17.674][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:17.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.676][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.677][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:17.678][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:17.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.680][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.681][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:17.683][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.693][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.694][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:17.695][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:17.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.697][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.698][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:17.699][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:17.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.701][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:17.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:17.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.706][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:17.707][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:17.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.709][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.710][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:17.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:17.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.714][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:17.715][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:17.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.716][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:17.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:17.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:17.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:17.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:17.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:17.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:17.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:17.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:17.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:17.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:17.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:17.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:17.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:17.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:17.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:17.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:17.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:17.754][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-01-02 20:19:17.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:17.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:17.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:17.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:17.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:17.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:17.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:17.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:17.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:17.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:17.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:17.784][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-01-02 20:19:17.785][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:17.786][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-01-02 20:19:17.787][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:17.788][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:17.789][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:17.790][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:17.791][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:17.792][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:17.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:17.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:17.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:17.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:17.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:17.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:17.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:17.804][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-01-02 20:19:17.807][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:17.808][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:17.809][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-01-02 20:19:18.153][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-01-02 20:19:18.503][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:18.505][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-01-02 20:19:18.508][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-01-02 20:19:18.511][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-01-02 20:19:18.512][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:18.513][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:18.514][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:18.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:18.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:18.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:18.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:18.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:18.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:18.524][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[2025-01-02 20:19:18.526][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:18.527][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:18.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.529][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:18.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:18.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.534][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:18.535][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:18.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.537][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.538][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:18.539][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:18.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.541][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.542][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:18.543][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:18.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.544][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.546][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:18.547][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:18.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.548][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.549][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:18.550][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:18.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.560][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.562][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:18.563][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.564][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.566][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:18.566][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:18.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.568][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.569][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:18.570][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:18.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.572][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:18.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:18.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.577][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:18.578][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:18.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.580][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.581][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:18.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:18.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.585][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:18.586][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:18.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.588][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:18.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:18.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:18.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:18.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:18.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:18.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:18.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:18.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:18.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:18.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:18.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:18.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:18.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:18.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:18.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:18.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:18.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:18.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:18.625][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-01-02 20:19:18.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:18.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:18.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:18.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:18.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:18.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:18.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:18.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:18.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:18.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:18.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:18.654][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-01-02 20:19:18.655][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:18.657][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-01-02 20:19:18.658][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:18.659][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:18.660][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:18.661][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:18.662][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:18.663][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:18.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:18.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:18.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:18.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:18.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:18.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:18.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:18.675][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-01-02 20:19:18.677][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:18.678][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:18.679][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-01-02 20:19:19.022][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-01-02 20:19:19.381][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-01-02 20:19:19.384][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-01-02 20:19:19.386][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-01-02 20:19:19.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-01-02 20:19:19.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-01-02 20:19:19.397][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:19.399][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:19.400][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:19.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:19.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:19.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:19.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:19.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:19.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:19.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:19.419][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:19.420][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:19.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.423][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:19.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:19.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.430][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:19.432][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:19.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.434][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.436][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:19.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:19.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.442][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:19.444][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:19.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.446][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:19.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:19.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.468][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:19.469][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:19.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.472][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:19.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:19.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.480][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:19.481][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:19.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.484][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:19.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:19.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.491][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:19.493][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:19.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.495][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.497][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:19.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:19.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.501][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:19.502][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:19.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.504][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.505][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:19.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:19.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.509][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:19.510][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:19.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.512][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:19.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:19.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.517][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:19.518][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:19.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.519][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.521][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:19.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:19.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.525][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:19.526][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:19.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.528][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.529][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:19.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:19.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.533][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:19.534][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:19.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.535][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.537][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:19.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:19.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:19.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:19.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:19.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:19.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:19.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:19.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:19.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:19.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:19.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:19.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:19.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:19.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:19.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:19.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:19.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:19.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:19.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:19.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:19.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:19.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:19.578][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-01-02 20:19:19.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:19.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:19.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:19.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:19.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:19.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:19.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:19.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:19.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:19.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:19.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:19.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:19.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:19.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:19.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:19.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:19.601][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-01-02 20:19:19.602][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:19.603][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-01-02 20:19:19.605][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:19.606][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:19.607][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:19.608][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:19.609][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:19.610][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:19.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:19.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:19.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:19.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:19.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:19.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:19.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:19.622][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-01-02 20:19:19.625][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:19.626][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:19.627][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-01-02 20:19:19.979][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-01-02 20:19:20.339][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:20.343][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-01-02 20:19:20.350][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-01-02 20:19:20.356][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-01-02 20:19:20.359][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:20.361][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:20.364][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:20.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:20.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:20.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:20.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:20.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:20.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:20.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:20.401][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:20.402][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:20.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.405][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:20.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:20.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.411][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:20.413][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:20.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.415][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.416][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:20.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:20.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.421][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:20.422][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:20.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.430][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.432][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:20.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:20.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.437][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:20.438][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:20.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.440][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:20.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:20.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.446][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:20.447][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:20.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.449][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.450][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:20.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:20.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.454][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:20.455][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:20.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.457][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.459][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:20.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:20.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.463][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:20.464][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:20.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.466][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.467][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:20.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:20.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:20.473][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:20.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.475][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:20.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:20.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.481][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:20.482][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:20.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.484][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:20.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:20.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.490][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:20.491][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:20.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.493][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.494][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:20.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:20.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.498][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:20.499][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:20.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.501][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.502][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:20.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:20.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:20.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:20.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:20.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:20.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:20.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:20.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:20.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:20.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:20.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:20.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:20.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:20.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:20.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:20.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:20.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:20.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:20.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:20.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:20.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:20.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:20.548][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-01-02 20:19:20.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:20.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:20.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:20.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:20.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:20.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:20.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:20.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:20.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:20.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:20.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:20.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:20.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:20.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:20.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:20.584][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[2025-01-02 20:19:20.586][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-01-02 20:19:20.587][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:20.590][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-01-02 20:19:20.592][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:20.594][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:20.595][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:20.597][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:20.598][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:20.599][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:20.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:20.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:20.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:20.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:20.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:20.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:20.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:20.660][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-01-02 20:19:20.664][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:20.665][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:20.667][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-01-02 20:19:21.012][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-01-02 20:19:21.389][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:21.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-01-02 20:19:21.403][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-01-02 20:19:21.410][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-01-02 20:19:21.413][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:21.417][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:21.420][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:21.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:21.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:21.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:21.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:21.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:21.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:21.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:21.446][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:21.448][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:21.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.450][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:21.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:21.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.457][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:21.458][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:21.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.461][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.462][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:21.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:21.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.467][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:21.468][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:21.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.470][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:21.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:21.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.476][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:21.477][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:21.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.478][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:21.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:21.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:21.484][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:21.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.486][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:21.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:21.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.491][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:21.492][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:21.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.494][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.495][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:21.496][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:21.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.498][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.499][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:21.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:21.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.503][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:21.503][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:21.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.505][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:21.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:21.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.510][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:21.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:21.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.513][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:21.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:21.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.518][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:21.519][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:21.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.520][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.521][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:21.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:21.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.525][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:21.526][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:21.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.528][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.529][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:21.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:21.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:21.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:21.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:21.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:21.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:21.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:21.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:21.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:21.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:21.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:21.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:21.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:21.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:21.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:21.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:21.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:21.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:21.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:21.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:21.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:21.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:21.570][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-01-02 20:19:21.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:21.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:21.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:21.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:21.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:21.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:21.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:21.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:21.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:21.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:21.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:21.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:21.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:21.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:21.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:21.603][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[2025-01-02 20:19:21.604][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-01-02 20:19:21.605][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:21.607][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.INFO [2025-01-02 20:19:21.608][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-01-02 20:19:21.609][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:21.610][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:21.611][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:21.612][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:21.613][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:21.614][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:21.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:21.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:21.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:21.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:21.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:21.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:21.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:21.627][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-01-02 20:19:21.630][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:21.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:21.632][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-01-02 20:19:21.975][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-01-02 20:19:22.332][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:22.337][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-01-02 20:19:22.344][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-01-02 20:19:22.350][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-01-02 20:19:22.353][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:22.356][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:22.359][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:22.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:22.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:22.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:22.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:22.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:22.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:22.382][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.TRACE[2025-01-02 20:19:22.386][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:22.388][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:22.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.391][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:22.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:22.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.399][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:22.400][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:22.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.403][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.404][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:22.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:22.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.409][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:22.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:22.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.413][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:22.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:22.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.419][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:22.420][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:22.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.422][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:22.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:22.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.427][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:22.428][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:22.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.430][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:22.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:22.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.435][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:22.437][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:22.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.438][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.440][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:22.441][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:22.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.443][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.444][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:22.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:22.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.448][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:22.449][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:22.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.451][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:22.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:22.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.456][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:22.457][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:22.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.459][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:22.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:22.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.465][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:22.466][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:22.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.468][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.469][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:22.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:22.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.473][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:22.474][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:22.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.476][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.477][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:22.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:22.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:22.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:22.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:22.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:22.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:22.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:22.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:22.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:22.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:22.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:22.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:22.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:22.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:22.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:22.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:22.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:22.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:22.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:22.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:22.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:22.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:22.529][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-01-02 20:19:22.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:22.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:22.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:22.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:22.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:22.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:22.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:22.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:22.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:22.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:22.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:22.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:22.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:22.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:22.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:22.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:22.552][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-01-02 20:19:22.554][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:22.555][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-01-02 20:19:22.556][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:22.558][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:22.559][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:22.560][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:22.561][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:22.562][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:22.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:22.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:22.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:22.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:22.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:22.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:22.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:22.575][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-01-02 20:19:22.578][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:22.579][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:22.580][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-01-02 20:19:22.932][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-01-02 20:19:23.284][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:23.288][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-01-02 20:19:23.296][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-01-02 20:19:23.302][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-01-02 20:19:23.305][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:23.308][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:23.310][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:23.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:23.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:23.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:23.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:23.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:23.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:23.332][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.TRACE[2025-01-02 20:19:23.336][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:23.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:23.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.340][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:23.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:23.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.348][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:23.349][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:23.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.352][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.353][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:23.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:23.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.358][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:23.360][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:23.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.362][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.363][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:23.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:23.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.368][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:23.369][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:23.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.371][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:23.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:23.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.376][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:23.377][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:23.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.379][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:23.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:23.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.384][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:23.385][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:23.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.387][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.389][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:23.390][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:23.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.392][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.393][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:23.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:23.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.397][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:23.398][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:23.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.400][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:23.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:23.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.405][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:23.406][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:23.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.408][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:23.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:23.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.413][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:23.414][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:23.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.416][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.417][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:23.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:23.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.421][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:23.422][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:23.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.424][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.425][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:23.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:23.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:23.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:23.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:23.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:23.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:23.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:23.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:23.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:23.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:23.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:23.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:23.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:23.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:23.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:23.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:23.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:23.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:23.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:23.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:23.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:23.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:23.479][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-01-02 20:19:23.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:23.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:23.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:23.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:23.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:23.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:23.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:23.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:23.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:23.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:23.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:23.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:23.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:23.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:23.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:23.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:23.503][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-01-02 20:19:23.504][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:23.506][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-01-02 20:19:23.507][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:23.508][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:23.510][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:23.511][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:23.512][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:23.513][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:23.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:23.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:23.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:23.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:23.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:23.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:23.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:23.527][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-01-02 20:19:23.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:23.530][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:23.532][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-01-02 20:19:23.875][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-01-02 20:19:24.230][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:24.232][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-01-02 20:19:24.235][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-01-02 20:19:24.238][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-01-02 20:19:24.239][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:24.241][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:24.242][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:24.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:24.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:24.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:24.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:24.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:24.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:24.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:24.255][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:24.256][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:24.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.258][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:24.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:24.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.263][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:24.264][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:24.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.266][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.267][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:24.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:24.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.271][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:24.272][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:24.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.274][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.276][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:24.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:24.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.280][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:24.281][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:24.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.283][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:24.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:24.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.288][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:24.289][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:24.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.291][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:24.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:24.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.296][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:24.297][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:24.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.298][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.300][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:24.301][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:24.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.302][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.304][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:24.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:24.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.308][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:24.309][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:24.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.310][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:24.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:24.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.315][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:24.316][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:24.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.318][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.319][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:24.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:24.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.334][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:24.335][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:24.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.337][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.339][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:24.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:24.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.342][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:24.343][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:24.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.345][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.347][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:24.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:24.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:24.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:24.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:24.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:24.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:24.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:24.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:24.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:24.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:24.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:24.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:24.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:24.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:24.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:24.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:24.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:24.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:24.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:24.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:24.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:24.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:24.391][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-01-02 20:19:24.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:24.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:24.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:24.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:24.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:24.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:24.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:24.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:24.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:24.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:24.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:24.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:24.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:24.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:24.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:24.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:24.415][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-01-02 20:19:24.416][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:24.418][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-01-02 20:19:24.419][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:24.420][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:24.421][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:24.422][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:24.423][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:24.424][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:24.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:24.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:24.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:24.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:24.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:24.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:24.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:24.438][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-01-02 20:19:24.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:24.442][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:24.444][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-01-02 20:19:24.787][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-01-02 20:19:25.146][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:25.149][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-01-02 20:19:25.154][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-01-02 20:19:25.158][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-01-02 20:19:25.160][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:25.162][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:25.163][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:25.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:25.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:25.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:25.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:25.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:25.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:25.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:25.184][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:25.185][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:25.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.188][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:25.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.196][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:25.197][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:25.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.200][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.202][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:25.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:25.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.208][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:25.210][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:25.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.213][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:25.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:25.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.221][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:25.223][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:25.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.225][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:25.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:25.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.233][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:25.235][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:25.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.238][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:25.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:25.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.246][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:25.247][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:25.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.304][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.306][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:25.307][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:25.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.309][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.310][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:25.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:25.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.314][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:25.315][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:25.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.317][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:25.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:25.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.322][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:25.323][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:25.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.325][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:25.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.330][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:25.331][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:25.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.333][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.334][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:25.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:25.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.338][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:25.339][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:25.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.341][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.343][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:25.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:25.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:25.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:25.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:25.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:25.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:25.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:25.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:25.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:25.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:25.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:25.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:25.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:25.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:25.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:25.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:25.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:25.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:25.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:25.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:25.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:25.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:25.383][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-01-02 20:19:25.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:25.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:25.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:25.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:25.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:25.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:25.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:25.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:25.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:25.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:25.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:25.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:25.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:25.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:25.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:25.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:25.406][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-01-02 20:19:25.407][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:25.408][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-01-02 20:19:25.409][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:25.410][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:25.411][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:25.412][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:25.413][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:25.414][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:25.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:25.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:25.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:25.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:25.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:25.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:25.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:25.427][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-01-02 20:19:25.430][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:25.431][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:25.433][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-01-02 20:19:25.776][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-01-02 20:19:26.122][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:26.126][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-01-02 20:19:26.132][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-01-02 20:19:26.136][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-01-02 20:19:26.139][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:26.141][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:26.143][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:26.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:26.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:26.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:26.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:26.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:26.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:26.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:26.165][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:26.167][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:26.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.169][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:26.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:26.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.177][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:26.178][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:26.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.181][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.182][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:26.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:26.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.187][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:26.188][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:26.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.190][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:26.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:26.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.207][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:26.208][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:26.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.210][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.211][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:26.212][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:26.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.214][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.215][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:26.216][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:26.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.218][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.219][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:26.220][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:26.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.222][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.224][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:26.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:26.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.228][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:26.229][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:26.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.230][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:26.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:26.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.236][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:26.237][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:26.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.239][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:26.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:26.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.244][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:26.245][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:26.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.247][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.248][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:26.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:26.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.252][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:26.253][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:26.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.255][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:26.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:26.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:26.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:26.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:26.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:26.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:26.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:26.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:26.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:26.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:26.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:26.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:26.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:26.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:26.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:26.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:26.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:26.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:26.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:26.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:26.296][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-01-02 20:19:26.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:26.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:26.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:26.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:26.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:26.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:26.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:26.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:26.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:26.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:26.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:26.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:26.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:26.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:26.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:26.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:26.319][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-01-02 20:19:26.320][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:26.322][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-01-02 20:19:26.323][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:26.324][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:26.325][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:26.326][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:26.327][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:26.328][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:26.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:26.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:26.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:26.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:26.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:26.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:26.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:26.341][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-01-02 20:19:26.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:26.344][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:26.346][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-01-02 20:19:26.692][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-01-02 20:19:27.039][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:27.044][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-01-02 20:19:27.051][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-01-02 20:19:27.057][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-01-02 20:19:27.060][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:27.063][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:27.065][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:27.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:27.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:27.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:27.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:27.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:27.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:27.088][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[2025-01-02 20:19:27.092][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:27.093][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:27.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.096][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:27.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:27.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.104][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:27.106][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:27.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.119][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.121][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:27.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:27.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.125][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:27.126][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:27.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.128][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:27.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:27.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.133][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:27.134][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:27.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.136][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.138][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:27.139][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:27.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.140][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.142][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:27.143][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:27.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.145][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.146][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:27.147][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:27.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.149][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.150][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:27.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:27.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.154][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:27.155][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:27.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.157][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:27.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:27.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.163][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:27.164][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:27.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.166][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.167][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:27.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:27.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.171][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:27.172][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:27.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.174][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.175][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:27.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:27.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.180][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:27.181][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:27.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.183][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:27.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:27.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:27.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:27.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:27.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:27.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:27.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:27.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:27.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:27.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:27.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:27.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:27.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:27.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:27.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:27.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:27.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:27.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:27.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:27.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:27.224][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-01-02 20:19:27.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:27.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:27.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:27.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:27.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:27.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:27.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:27.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:27.237][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:27.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:27.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:27.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:27.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:27.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:27.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:27.247][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-01-02 20:19:27.248][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:27.250][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-01-02 20:19:27.251][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:27.252][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:27.253][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:27.254][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:27.255][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:27.256][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:27.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:27.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:27.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:27.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:27.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:27.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:27.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:27.269][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-01-02 20:19:27.272][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:27.273][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:27.274][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-01-02 20:19:27.633][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-01-02 20:19:27.992][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:27.994][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-01-02 20:19:27.997][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-01-02 20:19:28.000][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-01-02 20:19:28.001][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:28.002][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:28.003][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:28.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:28.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:28.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:28.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:28.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:28.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:28.014][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[2025-01-02 20:19:28.028][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.029][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.031][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.036][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:28.037][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:28.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.039][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.040][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:28.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:28.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.044][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:28.045][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:28.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.047][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:28.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:28.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:28.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:28.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.055][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:28.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.060][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:28.061][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:28.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.062][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:28.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:28.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.067][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:28.068][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:28.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.070][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.071][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:28.072][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:28.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.074][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.075][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:28.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:28.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.079][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:28.079][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:28.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.081][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:28.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:28.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.086][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:28.087][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:28.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.089][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:28.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:28.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.094][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:28.095][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:28.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.096][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.098][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:28.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:28.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.101][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:28.102][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:28.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.104][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.105][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:28.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:28.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:28.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:28.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:28.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:28.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:28.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:28.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:28.146][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-01-02 20:19:28.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:28.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:28.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:28.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:28.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:28.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:28.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:28.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:28.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:28.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:28.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:28.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:28.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:28.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:28.169][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-01-02 20:19:28.170][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:28.171][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-01-02 20:19:28.173][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:28.174][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:28.175][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:28.176][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:28.177][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:28.178][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:28.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:28.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:28.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:28.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:28.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:28.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:28.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:28.190][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-01-02 20:19:28.193][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:28.194][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:28.195][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-01-02 20:19:28.546][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-01-02 20:19:28.908][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:28.912][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-01-02 20:19:28.917][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-01-02 20:19:28.921][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-01-02 20:19:28.923][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:28.925][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:28.927][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:28.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:28.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:28.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:28.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:28.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:28.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:28.944][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.TRACE[2025-01-02 20:19:28.948][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.949][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.952][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:28.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:28.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.960][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:28.962][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:28.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.965][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.966][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:28.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:28.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.972][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:28.974][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:28.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.977][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.979][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:28.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:28.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.985][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:28.987][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:28.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.989][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:28.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:28.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:28.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:28.998][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:28.999][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:29.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.002][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:29.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:29.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.010][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:29.012][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:29.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.015][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.016][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:29.018][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.021][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.023][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:29.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.030][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:29.031][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:29.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.033][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:29.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:29.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.038][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:29.039][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:29.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.041][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:29.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:29.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.047][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:29.048][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:29.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.050][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.051][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:29.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:29.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.055][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:29.056][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:29.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.058][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.059][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:29.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:29.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:29.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:29.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:29.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:29.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:29.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:29.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:29.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:29.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:29.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:29.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:29.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:29.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:29.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:29.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:29.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:29.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:29.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:29.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:29.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:29.102][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-01-02 20:19:29.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:29.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:29.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:29.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:29.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:29.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:29.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:29.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:29.124][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-01-02 20:19:29.126][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:29.127][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-01-02 20:19:29.128][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:29.129][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:29.140][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:29.141][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:29.142][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:29.143][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:29.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:29.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:29.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:29.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:29.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:29.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:29.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:29.156][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-01-02 20:19:29.159][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:29.160][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:29.161][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-01-02 20:19:29.522][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-01-02 20:19:29.881][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:29.885][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-01-02 20:19:29.891][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-01-02 20:19:29.895][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-01-02 20:19:29.897][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:29.899][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:29.901][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:29.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:29.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:29.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:29.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:29.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:29.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:29.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:29.918][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:29.920][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:29.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.922][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:29.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:29.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.928][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:29.929][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:29.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.931][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.932][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:29.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:29.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.937][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:29.938][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:29.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.940][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.941][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:29.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:29.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.945][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:29.946][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:29.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.949][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:29.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:29.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.954][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:29.955][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:29.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.957][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:29.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:29.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.963][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:29.964][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:29.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.966][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.967][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:29.968][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.970][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.972][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:29.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:29.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.976][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:29.977][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:29.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.979][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:29.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:29.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.984][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:29.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:29.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.987][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:29.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:29.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.992][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:29.993][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:29.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.995][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:29.996][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:29.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:29.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:29.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.000][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:30.001][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:30.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.003][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.004][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:30.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:30.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:30.047][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-01-02 20:19:30.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:30.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:30.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:30.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:30.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:30.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:30.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:30.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:30.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:30.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:30.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:30.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:30.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:30.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:30.080][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-01-02 20:19:30.081][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:30.082][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-01-02 20:19:30.083][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:30.084][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:30.086][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:30.087][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:30.088][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:30.089][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:30.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:30.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:30.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:30.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:30.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:30.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:30.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:30.102][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-01-02 20:19:30.105][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:30.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:30.107][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-01-02 20:19:30.456][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-01-02 20:19:30.808][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:30.812][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-01-02 20:19:30.820][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-01-02 20:19:30.826][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-01-02 20:19:30.829][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:30.832][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:30.834][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:30.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:30.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:30.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:30.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:30.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:30.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:30.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:30.861][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.862][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.865][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.873][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:30.875][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:30.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.878][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.879][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:30.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:30.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.885][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:30.886][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:30.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.888][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:30.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.895][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:30.896][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:30.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.898][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:30.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:30.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.904][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:30.905][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:30.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.907][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:30.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:30.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.913][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:30.914][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:30.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.916][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.917][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:30.918][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:30.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.920][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.922][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:30.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:30.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.926][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:30.927][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:30.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.928][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:30.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:30.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.934][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:30.935][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:30.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.936][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:30.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:30.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.942][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:30.943][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:30.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.945][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.946][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:30.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:30.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.950][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:30.951][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:30.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.953][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.954][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:30.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:30.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:30.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:30.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:30.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:30.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:30.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:31.007][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-01-02 20:19:31.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:31.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:31.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:31.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:31.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:31.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:31.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:31.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:31.030][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-01-02 20:19:31.031][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:31.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-01-02 20:19:31.034][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:31.035][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:31.036][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:31.037][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:31.038][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:31.039][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:31.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:31.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:31.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:31.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:31.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:31.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:31.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:31.053][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-01-02 20:19:31.055][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:31.056][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:31.058][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-01-02 20:19:31.401][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-01-02 20:19:31.751][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:31.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-01-02 20:19:31.757][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-01-02 20:19:31.760][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-01-02 20:19:31.761][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:31.762][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:31.763][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:31.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:31.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:31.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:31.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:31.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:31.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:31.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:31.777][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.778][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.780][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.785][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:31.786][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:31.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.788][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.789][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:31.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:31.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.793][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:31.794][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:31.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.796][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.798][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:31.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:31.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.802][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:31.803][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:31.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.805][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:31.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:31.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.810][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:31.811][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:31.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.813][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:31.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:31.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.818][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:31.819][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:31.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.821][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.822][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:31.823][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.825][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.826][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:31.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.830][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:31.831][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:31.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.833][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:31.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:31.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.838][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:31.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:31.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.841][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:31.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:31.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.846][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:31.847][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:31.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.849][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.850][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:31.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:31.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.854][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:31.855][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:31.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.857][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.858][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:31.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:31.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:31.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:31.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:31.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:31.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:31.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:31.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:31.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:31.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:31.913][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-01-02 20:19:31.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:31.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:31.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:31.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:31.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:31.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:31.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:31.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:31.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:31.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:31.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:31.936][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-01-02 20:19:31.937][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:31.939][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-01-02 20:19:31.940][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:31.941][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:31.943][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:31.944][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:31.945][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:31.946][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:31.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:31.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:31.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:31.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:31.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:31.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:31.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:31.959][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-01-02 20:19:31.962][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:31.963][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:31.964][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-01-02 20:19:32.305][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-01-02 20:19:32.649][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:32.654][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-01-02 20:19:32.661][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-01-02 20:19:32.666][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-01-02 20:19:32.669][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:32.672][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:32.675][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:32.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:32.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:32.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:32.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:32.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:32.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:32.697][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.TRACE[2025-01-02 20:19:32.701][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:32.702][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:32.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.706][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:32.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:32.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.713][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:32.715][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:32.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.717][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.719][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:32.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:32.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.724][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:32.725][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:32.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.727][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:32.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:32.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.733][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:32.735][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:32.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.737][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:32.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:32.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.742][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:32.743][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:32.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.745][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:32.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:32.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.750][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:32.751][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:32.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.752][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.754][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:32.755][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:32.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.756][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.757][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:32.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:32.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.761][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:32.762][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:32.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.764][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:32.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:32.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.780][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:32.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:32.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.783][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:32.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:32.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.788][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:32.789][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:32.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.791][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.792][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:32.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:32.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.796][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:32.797][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:32.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.799][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.800][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:32.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:32.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:32.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:32.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:32.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:32.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:32.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:32.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:32.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:32.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:32.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:32.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:32.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:32.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:32.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:32.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:32.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:32.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:32.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:32.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:32.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:32.840][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-01-02 20:19:32.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:32.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:32.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:32.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:32.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:32.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:32.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:32.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:32.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:32.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:32.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:32.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:32.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:32.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:32.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:32.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:32.862][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-01-02 20:19:32.863][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:32.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-01-02 20:19:32.865][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:32.866][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:32.867][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:32.868][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:32.869][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:32.870][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:32.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:32.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:32.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:32.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:32.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:32.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:32.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:32.883][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-01-02 20:19:32.886][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:32.886][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:32.888][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-01-02 20:19:33.229][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-01-02 20:19:33.577][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:33.582][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-01-02 20:19:33.590][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-01-02 20:19:33.595][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-01-02 20:19:33.598][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:33.601][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:33.604][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:33.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:33.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:33.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:33.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:33.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:33.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:33.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:33.630][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:33.632][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:33.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.635][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:33.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:33.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.643][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:33.644][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:33.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.646][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.648][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:33.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:33.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.653][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:33.654][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:33.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.656][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.658][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:33.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:33.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.662][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:33.663][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:33.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.665][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:33.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:33.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.677][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:33.683][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:33.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.685][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.686][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:33.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:33.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.690][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:33.691][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:33.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.693][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.694][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:33.695][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:33.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.697][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.698][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:33.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:33.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.702][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:33.703][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:33.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.705][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:33.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:33.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.710][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:33.711][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:33.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.713][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:33.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:33.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.719][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:33.720][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:33.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.722][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.723][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:33.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:33.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.727][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:33.728][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:33.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.730][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.731][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:33.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:33.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:33.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:33.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:33.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:33.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:33.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:33.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:33.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:33.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:33.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:33.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:33.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:33.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:33.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:33.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:33.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:33.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:33.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:33.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:33.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:33.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:33.775][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-01-02 20:19:33.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:33.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:33.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:33.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:33.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:33.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:33.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:33.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:33.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:33.805][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:33.808][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:33.809][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:33.811][private$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[2025-01-02 20:19:34.353][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[2025-01-02 20:19:34.897][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:34.901][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-01-02 20:19:34.908][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-01-02 20:19:34.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:34.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:34.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:34.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:34.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:34.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:34.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:34.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:34.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:34.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:34.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:34.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:34.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:34.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:34.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:34.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:34.944][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.TRACE[2025-01-02 20:19:34.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:34.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:34.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:34.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:34.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:34.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:34.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:34.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:34.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:34.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:34.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:34.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:34.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:34.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:34.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:34.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:34.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:34.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.047][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.TRACE[2025-01-02 20:19:35.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.193][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[2025-01-02 20:19:35.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.228][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.TRACE[2025-01-02 20:19:35.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.264][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[2025-01-02 20:19:35.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.313][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[2025-01-02 20:19:35.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.355][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.TRACE[2025-01-02 20:19:35.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.382][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.TRACE[2025-01-02 20:19:35.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:35.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:35.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:35.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:35.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:35.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:35.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:35.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:35.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:35.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:35.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:35.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:35.500][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:35.504][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:35.505][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:35.507][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-02 20:19:35.843][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:36.189][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:36.193][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-01-02 20:19:36.201][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-01-02 20:19:36.207][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:36.214][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:36.216][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:36.220][private$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[2025-01-02 20:19:36.566][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:36.908][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:36.913][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-01-02 20:19:36.921][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-01-02 20:19:36.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:36.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:36.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:36.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:36.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:36.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:36.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:36.967][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-01-02 20:19:36.968][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:36.971][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-01-02 20:19:36.972][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:36.974][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:36.975][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:36.977][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:36.978][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:36.979][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:36.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:36.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:36.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:36.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:36.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:36.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:36.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:36.999][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-01-02 20:19:37.003][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:37.005][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:37.007][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-01-02 20:19:37.363][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-01-02 20:19:37.718][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:37.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-01-02 20:19:37.724][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-01-02 20:19:37.727][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-01-02 20:19:37.728][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:37.730][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:37.731][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:37.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:37.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:37.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:37.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:37.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:37.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:37.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:37.744][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:37.745][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:37.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.747][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:37.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:37.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.752][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:37.753][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:37.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.755][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.757][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:37.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:37.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.761][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:37.762][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:37.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.763][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.765][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:37.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:37.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.769][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:37.770][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:37.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.772][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:37.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:37.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.777][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:37.778][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:37.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.780][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:37.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:37.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.785][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:37.786][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:37.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.787][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.789][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:37.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:37.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.793][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:37.794][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:37.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.795][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.797][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:37.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:37.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.801][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.802][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.803][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.809][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:37.810][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:37.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.812][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:37.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:37.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.817][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:37.818][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:37.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.820][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.821][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:37.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:37.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.825][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:37.826][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:37.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.828][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.829][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:37.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:37.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:37.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:37.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:37.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:37.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:37.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:37.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:37.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:37.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:37.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:37.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:37.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:37.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:37.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:37.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:37.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:37.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:37.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:37.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:37.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:37.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:37.883][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-01-02 20:19:37.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:37.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:37.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:37.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:37.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:37.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:37.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:37.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:37.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:37.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:37.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:37.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:37.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:37.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:37.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:37.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:37.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:37.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:37.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:37.927][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-01-02 20:19:37.928][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:37.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-01-02 20:19:37.931][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:37.932][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:37.933][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:37.934][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:37.935][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:37.936][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:37.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:37.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:37.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:37.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:37.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:37.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:37.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:37.949][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-01-02 20:19:37.951][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:37.952][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:37.954][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-01-02 20:19:38.293][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-01-02 20:19:38.636][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:38.638][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-01-02 20:19:38.642][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-01-02 20:19:38.645][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-01-02 20:19:38.646][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:38.647][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:38.649][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:38.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:38.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:38.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:38.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:38.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:38.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:38.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:38.663][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:38.664][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:38.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.666][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:38.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:38.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.671][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:38.672][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:38.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.674][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.676][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:38.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:38.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.680][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:38.681][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:38.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.683][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.684][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:38.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:38.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.688][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:38.689][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:38.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.691][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:38.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:38.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.696][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:38.697][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:38.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.699][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:38.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:38.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.704][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:38.705][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:38.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.707][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.709][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:38.710][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:38.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.711][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.713][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:38.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:38.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.717][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.718][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.720][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.725][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:38.726][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:38.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.741][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:38.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:38.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.748][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:38.749][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:38.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.751][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.752][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:38.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:38.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.756][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:38.757][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:38.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.759][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.760][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:38.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:38.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:38.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:38.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:38.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:38.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:38.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:38.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:38.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:38.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:38.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:38.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:38.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:38.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:38.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:38.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:38.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:38.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:38.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:38.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:38.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:38.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:38.805][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-01-02 20:19:38.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:38.836][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[2025-01-02 20:19:38.839][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:38.841][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-02 20:19:38.842][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:38.843][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-02 20:19:38.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:38.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:38.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:38.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:38.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:38.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:38.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:38.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:38.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:38.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:38.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:38.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:38.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:38.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:38.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:38.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:38.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:38.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:38.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:38.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:38.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:38.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:38.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:38.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:38.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:38.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:38.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:38.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:38.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:38.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:38.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:38.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:38.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:38.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:38.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:38.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:38.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:38.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:38.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:38.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:38.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:38.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:38.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:38.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:38.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:38.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:38.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:38.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:38.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:38.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:38.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.017][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.TRACE[2025-01-02 20:19:39.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.083][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.TRACE[2025-01-02 20:19:39.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.177][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.TRACE[2025-01-02 20:19:39.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.200][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[2025-01-02 20:19:39.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.349][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[2025-01-02 20:19:39.352][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:39.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-02 20:19:39.355][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:39.357][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-02 20:19:39.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.451][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[2025-01-02 20:19:39.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.577][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.TRACE[2025-01-02 20:19:39.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.620][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.TRACE[2025-01-02 20:19:39.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.717][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.TRACE[2025-01-02 20:19:39.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:39.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:39.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.862][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-02 20:19:39.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-02 20:19:39.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:39.874][biodb::testThat]
biodb.INFO [2025-01-02 20:19:39.875][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-01-02 20:19:39.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:39.877][biodb::testThat]
biodb.TRACE[2025-01-02 20:19:39.880][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-02 20:19:39.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-02 20:19:39.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:39.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:39.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:39.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:39.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:39.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:39.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:39.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:39.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:39.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:39.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:39.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:39.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:39.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:39.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:39.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:39.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:39.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:39.916][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[2025-01-02 20:19:39.919][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:39.920][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:39.922][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-02 20:19:40.267][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:40.615][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:40.618][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-01-02 20:19:40.622][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-01-02 20:19:40.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:40.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:40.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:40.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:40.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:40.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:40.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:40.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:40.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:40.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:40.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:40.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:40.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:40.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:40.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:40.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:40.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:40.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:40.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:40.650][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:40.654][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:40.655][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:40.657][private$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[2025-01-02 20:19:40.998][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[2025-01-02 20:19:41.343][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:41.348][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-01-02 20:19:41.356][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-01-02 20:19:41.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:41.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:41.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:41.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:41.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:41.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:41.382][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.TRACE[2025-01-02 20:19:41.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:41.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:41.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:41.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:41.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:41.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:41.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:41.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:41.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:41.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:41.431][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-02 20:19:41.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:41.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:41.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:41.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:41.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:41.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:41.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:41.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.465][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.466][private$selectFields]
biodb.TRACE[2025-01-02 20:19:41.467][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:41.468][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:41.469][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.470][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.472][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.473][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.476][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.477][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.478][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.479][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.480][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.482][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.483][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:41.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.505][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-02 20:19:41.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:41.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:41.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:41.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:41.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:41.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:41.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:41.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.525][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.526][private$selectFields]
biodb.TRACE[2025-01-02 20:19:41.527][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:41.528][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:41.529][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.530][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.533][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.534][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.535][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.537][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.538][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.539][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.540][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.541][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.543][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.544][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:41.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.557][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-02 20:19:41.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:41.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:41.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:41.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:41.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:41.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:41.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:41.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.577][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.578][private$selectFields]
biodb.TRACE[2025-01-02 20:19:41.579][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:41.580][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:41.581][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.582][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.583][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.584][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.585][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.586][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.588][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.589][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.590][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:41.591][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.592][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.594][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.595][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:41.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:41.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.608][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-02 20:19:41.609][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-02 20:19:41.610][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-02 20:19:41.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:41.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:41.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:41.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:41.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:41.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:41.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:41.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:41.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:41.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:41.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:41.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:41.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:41.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:41.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:41.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:41.707][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[2025-01-02 20:19:41.711][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[2025-01-02 20:19:41.714][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:41.715][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:41.718][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-02 20:19:42.066][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:42.408][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:42.413][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-01-02 20:19:42.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-01-02 20:19:42.427][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:42.434][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:42.436][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:42.440][private$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[2025-01-02 20:19:42.786][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[2025-01-02 20:19:43.156][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:43.160][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-01-02 20:19:43.169][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-01-02 20:19:43.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.195][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.TRACE[2025-01-02 20:19:43.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.304][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-02 20:19:43.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.339][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[2025-01-02 20:19:43.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.348][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.349][private$selectFields]
biodb.TRACE[2025-01-02 20:19:43.350][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:43.351][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:43.352][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.353][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.354][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.356][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.357][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.358][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.360][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.361][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.362][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.363][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.364][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.366][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.367][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:43.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.381][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-02 20:19:43.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.440][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.441][private$selectFields]
biodb.TRACE[2025-01-02 20:19:43.442][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:43.443][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:43.444][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.445][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.446][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.448][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.449][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.450][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.451][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.452][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.463][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.464][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.465][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.467][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.468][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:43.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.481][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-02 20:19:43.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.501][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.502][private$selectFields]
biodb.TRACE[2025-01-02 20:19:43.503][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:43.504][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:43.505][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.506][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.507][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.509][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.510][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.511][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.513][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.514][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.515][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.515][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.516][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.518][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.519][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:43.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.532][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-02 20:19:43.533][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-02 20:19:43.534][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-02 20:19:43.542][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-02 20:19:43.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-02 20:19:43.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:43.549][biodb::testThat]
biodb.INFO [2025-01-02 20:19:43.550][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-01-02 20:19:43.551][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:43.552][biodb::testThat]
biodb.TRACE[2025-01-02 20:19:43.555][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-02 20:19:43.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-02 20:19:43.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:43.587][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[2025-01-02 20:19:43.590][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:43.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-02 20:19:43.593][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:43.594][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-02 20:19:43.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.625][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[2025-01-02 20:19:43.628][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:43.629][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-02 20:19:43.630][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:43.632][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-02 20:19:43.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.665][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[2025-01-02 20:19:43.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:43.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.679][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-02 20:19:43.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.690][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.TRACE[2025-01-02 20:19:43.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.699][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.700][private$selectFields]
biodb.TRACE[2025-01-02 20:19:43.701][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:43.702][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:43.702][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.703][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.705][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.706][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.707][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.708][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.710][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.711][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.712][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.713][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.714][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.716][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.717][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:43.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.730][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-02 20:19:43.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.749][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.750][private$selectFields]
biodb.TRACE[2025-01-02 20:19:43.751][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:43.752][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:43.753][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.754][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.755][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.757][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.758][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.759][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.760][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.761][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.762][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.763][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.764][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.766][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.767][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:43.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.780][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-02 20:19:43.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.806][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.807][private$selectFields]
biodb.TRACE[2025-01-02 20:19:43.808][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:43.809][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:43.810][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.811][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.812][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.813][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.814][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.815][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.817][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.818][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.819][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.820][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.821][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.823][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.824][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:43.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.837][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-02 20:19:43.838][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-02 20:19:43.839][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-02 20:19:43.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.875][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[2025-01-02 20:19:43.878][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[2025-01-02 20:19:43.881][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:43.883][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-01-02 20:19:43.884][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:43.885][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-01-02 20:19:43.889][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[2025-01-02 20:19:43.892][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:43.893][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-01-02 20:19:43.894][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:43.895][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-01-02 20:19:43.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:43.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:43.963][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-02 20:19:43.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:43.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:43.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:43.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:43.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:43.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:43.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:43.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.990][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.991][private$selectFields]
biodb.TRACE[2025-01-02 20:19:43.991][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:43.992][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:43.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:43.994][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.995][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:43.997][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:43.998][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:43.999][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.001][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.002][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.003][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.004][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.005][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.007][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.008][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:44.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.021][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-02 20:19:44.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.040][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.041][private$selectFields]
biodb.TRACE[2025-01-02 20:19:44.042][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:44.043][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:44.044][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.045][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.046][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.048][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.049][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.052][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.053][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.054][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.055][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.056][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.057][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.058][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:44.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.071][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-02 20:19:44.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.091][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.092][private$selectFields]
biodb.TRACE[2025-01-02 20:19:44.093][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:44.093][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:44.094][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.095][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.098][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.100][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.102][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.103][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.104][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.105][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.107][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.108][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:44.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.121][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-02 20:19:44.122][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-02 20:19:44.123][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-02 20:19:44.131][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-02 20:19:44.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-02 20:19:44.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:44.138][biodb::testThat]
biodb.INFO [2025-01-02 20:19:44.138][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-01-02 20:19:44.139][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:44.140][biodb::testThat]
biodb.TRACE[2025-01-02 20:19:44.143][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-02 20:19:44.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-02 20:19:44.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:44.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:44.184][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[2025-01-02 20:19:44.187][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:44.189][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-02 20:19:44.190][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:44.191][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-02 20:19:44.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:44.217][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[2025-01-02 20:19:44.220][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:44.222][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-02 20:19:44.223][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:44.224][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-02 20:19:44.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:44.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:44.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:44.271][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-02 20:19:44.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.282][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.TRACE[2025-01-02 20:19:44.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.290][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.291][private$selectFields]
biodb.TRACE[2025-01-02 20:19:44.292][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:44.293][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:44.294][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.295][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.296][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.298][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.298][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.299][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.301][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.302][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.303][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.304][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.305][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.307][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.308][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:44.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.320][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-02 20:19:44.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.345][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.346][private$selectFields]
biodb.TRACE[2025-01-02 20:19:44.347][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:44.347][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:44.348][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.349][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.350][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.352][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.353][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.354][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.356][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.357][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.358][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.359][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.360][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.362][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.363][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:44.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.376][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-02 20:19:44.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.395][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.396][private$selectFields]
biodb.TRACE[2025-01-02 20:19:44.397][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:44.397][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:44.398][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.399][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.400][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.402][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.403][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.404][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.406][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.407][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.408][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.412][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.413][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:44.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.426][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-02 20:19:44.427][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-02 20:19:44.428][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-02 20:19:44.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:44.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:44.476][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[2025-01-02 20:19:44.479][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:44.481][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-01-02 20:19:44.482][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:44.483][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-01-02 20:19:44.486][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[2025-01-02 20:19:44.489][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:44.490][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-01-02 20:19:44.491][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:44.492][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-01-02 20:19:44.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:44.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:44.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:44.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:44.567][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-02 20:19:44.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.577][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.TRACE[2025-01-02 20:19:44.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.587][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.588][private$selectFields]
biodb.TRACE[2025-01-02 20:19:44.589][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:44.589][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:44.590][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.591][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.592][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.594][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.595][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.596][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.598][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.599][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.600][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.601][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.602][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.604][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.605][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:44.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.618][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-02 20:19:44.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:44.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.636][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.637][private$selectFields]
biodb.TRACE[2025-01-02 20:19:44.638][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:44.639][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:44.640][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.641][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.642][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.644][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.645][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.646][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.647][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.648][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.649][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.650][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.651][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.653][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.654][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:44.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.667][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-02 20:19:44.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.676][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[2025-01-02 20:19:44.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.691][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.692][private$selectFields]
biodb.TRACE[2025-01-02 20:19:44.693][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-02 20:19:44.694][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-02 20:19:44.695][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.696][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.698][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.699][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.700][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.702][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.703][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.704][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-02 20:19:44.705][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.706][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.708][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.709][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-02 20:19:44.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:44.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:44.721][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-02 20:19:44.722][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-02 20:19:44.723][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-02 20:19:44.741][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-02 20:19:44.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-02 20:19:44.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:44.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:44.748][biodb::testThat]
biodb.INFO [2025-01-02 20:19:44.749][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-01-02 20:19:44.750][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:44.751][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:44.753][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-01-02 20:19:44.754][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:44.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-01-02 20:19:44.757][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:44.758][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:44.759][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:44.760][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:44.761][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:44.762][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:44.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:44.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:44.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:44.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:44.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:44.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:44.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:44.775][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-01-02 20:19:44.777][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:44.778][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:44.780][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-01-02 20:19:45.120][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-01-02 20:19:45.466][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:45.471][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-01-02 20:19:45.477][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-01-02 20:19:45.483][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-01-02 20:19:45.486][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:45.489][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:45.491][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:45.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:45.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:45.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:45.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:45.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:45.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:45.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:45.517][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:45.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:45.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.522][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:45.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:45.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.529][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:45.531][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:45.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.533][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.535][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:45.536][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:45.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.539][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.540][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:45.542][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:45.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.544][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.545][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:45.546][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:45.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.548][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.550][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:45.551][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:45.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.553][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.554][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:45.555][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:45.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.557][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.558][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:45.559][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:45.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.561][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.562][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:45.563][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:45.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.565][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.567][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:45.568][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:45.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.569][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.571][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:45.572][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:45.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.574][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:45.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:45.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:45.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:45.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:45.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:45.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:45.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:45.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:45.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:45.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:45.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:45.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:45.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:45.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:45.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:45.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:45.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:45.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:45.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:45.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:45.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:45.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:45.627][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-01-02 20:19:45.628][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-01-02 20:19:45.636][biodb::testThat]
biodb.INFO [2025-01-02 20:19:45.637][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-01-02 20:19:45.638][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:45.638][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:45.657][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-01-02 20:19:45.659][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-01-02 20:19:45.660][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-01-02 20:19:45.661][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-01-02 20:19:45.663][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-01-02 20:19:45.664][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:45.665][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:45.666][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:45.667][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:45.668][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:45.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:45.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:45.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:45.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:45.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:45.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:45.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:45.682][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-01-02 20:19:45.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:45.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:45.687][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-01-02 20:19:46.026][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-01-02 20:19:46.380][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:46.383][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-01-02 20:19:46.388][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-01-02 20:19:46.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:46.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:46.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:46.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:46.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:46.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:46.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:46.404][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-01-02 20:19:46.407][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:46.409][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:46.411][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-01-02 20:19:46.755][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-01-02 20:19:47.104][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:47.107][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-01-02 20:19:47.112][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-01-02 20:19:47.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:47.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:47.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:47.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:47.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:47.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:47.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:47.129][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-01-02 20:19:47.132][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:47.134][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:47.136][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-01-02 20:19:47.478][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-01-02 20:19:47.833][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:47.837][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-01-02 20:19:47.844][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-01-02 20:19:47.849][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-01-02 20:19:47.852][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:47.854][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-01-02 20:19:47.857][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:47.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:47.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:47.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:47.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:47.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:47.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:47.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:47.882][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:47.884][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:47.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.887][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:47.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.894][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:47.896][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:47.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.898][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.900][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:47.908][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:47.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.921][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.923][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:47.924][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:47.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.926][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.927][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:47.928][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:47.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.930][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.931][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:47.932][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:47.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.934][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.935][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:47.936][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:47.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.938][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.939][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:47.940][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:47.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.942][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.943][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:47.944][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:47.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.946][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.948][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:47.949][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:47.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.950][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.951][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:47.952][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:47.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.954][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:47.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:47.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:47.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:47.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:47.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:47.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:47.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:47.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:47.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:47.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:47.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:47.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:47.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:47.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:47.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:47.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:47.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:47.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:47.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:47.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:47.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:47.992][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:47.993][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:47.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.995][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:47.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:47.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:47.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:47.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.000][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:48.001][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:48.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.002][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.004][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:48.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:48.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.007][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:48.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:48.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.010][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:48.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:48.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.015][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:48.016][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:48.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.018][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:48.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:48.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.023][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:48.024][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:48.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.026][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:48.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:48.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.031][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:48.032][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:48.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.034][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.035][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:48.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:48.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.039][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:48.040][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:48.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.042][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.043][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:48.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:48.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.047][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:48.048][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:48.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.050][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:48.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:48.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.055][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:48.056][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:48.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.058][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.059][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:48.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:48.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.063][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:48.064][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:48.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.066][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.067][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:48.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:48.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.071][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:48.072][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:48.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.074][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.075][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:48.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:48.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:48.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:48.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:48.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:48.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:48.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:48.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:48.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:48.124][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.125][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.127][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.132][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:48.133][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:48.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.135][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.136][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:48.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:48.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.139][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:48.140][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:48.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.142][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.143][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:48.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:48.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.147][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:48.148][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:48.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.150][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.151][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:48.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:48.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.155][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:48.156][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:48.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.157][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.159][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:48.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:48.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.162][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:48.163][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:48.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.165][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.166][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:48.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:48.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.170][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:48.171][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:48.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.173][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.174][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:48.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:48.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.178][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:48.179][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:48.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.180][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:48.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:48.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.185][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:48.186][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:48.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.188][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:48.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:48.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.193][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:48.194][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:48.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.196][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.197][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:48.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:48.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.201][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:48.202][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:48.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.203][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.205][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:48.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:48.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:48.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:48.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:48.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:48.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:48.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:48.278][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-01-02 20:19:48.279][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-01-02 20:19:48.280][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-01-02 20:19:48.292][biodb::testThat]
biodb.INFO [2025-01-02 20:19:48.293][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-01-02 20:19:48.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:48.295][biodb::testThat]
biodb.INFO [2025-01-02 20:19:48.317][biodb::testThat]
biodb.INFO [2025-01-02 20:19:48.318][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-01-02 20:19:48.319][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:48.320][biodb::testThat]
biodb.INFO [2025-01-02 20:19:48.327][biodb::testThat]
biodb.INFO [2025-01-02 20:19:48.328][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-01-02 20:19:48.329][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:48.330][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:48.333][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[2025-01-02 20:19:48.336][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:48.337][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:48.338][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-01-02 20:19:48.798][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:49.300][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:49.307][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-01-02 20:19:49.316][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-01-02 20:19:49.336][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:49.339][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:49.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:49.342][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:49.343][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:49.345][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:49.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:49.348][ef$get] fields variable is a list.
biodb.INFO [2025-01-02 20:19:49.350][biodb::testThat]
biodb.INFO [2025-01-02 20:19:49.352][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-01-02 20:19:49.353][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:49.355][biodb::testThat]
biodb.ERROR[2025-01-02 20:19:49.372][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-01-02 20:19:49.390][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-01-02 20:19:49.404][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-02 20:19:49.405][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-02 20:19:49.407][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-02 20:19:49.408][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-02 20:19:49.408][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.410][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.412][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-02 20:19:49.436][biodb::testContext]
biodb.INFO [2025-01-02 20:19:49.438][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-02 20:19:49.439][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-01-02 20:19:49.440][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-02 20:19:49.441][biodb::testContext]
biodb.INFO [2025-01-02 20:19:49.443][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-02 20:19:49.445][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-02 20:19:49.449][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:49.450][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-02 20:19:49.451][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-02 20:19:49.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.455][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-02 20:19:49.456][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-02 20:19:49.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.459][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-02 20:19:49.460][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-02 20:19:49.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.464][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-02 20:19:49.465][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-02 20:19:49.466][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-02 20:19:49.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.470][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-02 20:19:49.471][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-02 20:19:49.472][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-02 20:19:49.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.475][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-02 20:19:49.476][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-02 20:19:49.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.480][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-02 20:19:49.481][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-02 20:19:49.482][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-02 20:19:49.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.486][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-02 20:19:49.487][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-02 20:19:49.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.490][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-02 20:19:49.491][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-02 20:19:49.492][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-02 20:19:49.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.496][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-02 20:19:49.497][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-02 20:19:49.498][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-02 20:19:49.499][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-02 20:19:49.500][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-02 20:19:49.501][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-02 20:19:49.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.505][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-02 20:19:49.506][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-02 20:19:49.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.508][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[2025-01-02 20:19:49.509][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-02 20:19:49.510][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-02 20:19:49.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.514][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-02 20:19:49.515][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-02 20:19:49.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.519][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-02 20:19:49.520][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-02 20:19:49.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.523][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-02 20:19:49.524][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-02 20:19:49.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.527][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[2025-01-02 20:19:49.528][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-02 20:19:49.529][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-02 20:19:49.532][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-02 20:19:49.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.536][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-02 20:19:49.537][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-02 20:19:49.538][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-02 20:19:49.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.541][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[2025-01-02 20:19:49.542][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-02 20:19:49.544][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.545][self$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[2025-01-02 20:19:49.546][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.547][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:49.548][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.549][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.550][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.551][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.552][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-02 20:19:49.553][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:49.554][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.555][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-02 20:19:49.556][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:49.557][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.558][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.559][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:49.559][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:49.559][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:49.559][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-02 20:19:49.559][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-02 20:19:49.560][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:49.561][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:49.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:49.562][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:49.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:49.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:49.565][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.566][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.567][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:49.568][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:49.569][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.570][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.571][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-02 20:19:49.573][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.574][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-02 20:19:49.575][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.576][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:49.577][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.578][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.579][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.580][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.581][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-02 20:19:49.582][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:49.583][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.583][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-02 20:19:49.585][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:49.586][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.587][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.587][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:49.587][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:49.587][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:49.587][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-02 20:19:49.587][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-02 20:19:49.588][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:49.589][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:49.590][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:49.591][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:49.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:49.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:49.594][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.595][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.596][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:49.597][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:49.598][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.599][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.600][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-02 20:19:49.602][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.603][self$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[2025-01-02 20:19:49.604][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.605][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:49.606][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.607][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.614][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.617][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-02 20:19:49.618][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:49.619][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.620][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-02 20:19:49.621][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:49.622][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.623][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.624][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.625][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:49.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:49.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:49.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:49.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:49.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:49.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.632][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.633][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:49.634][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:49.635][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.636][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.637][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-02 20:19:49.639][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.640][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-02 20:19:49.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:49.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.645][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.646][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.647][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-02 20:19:49.648][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:49.649][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.650][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-02 20:19:49.651][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:49.652][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.653][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:49.654][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.655][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:49.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:49.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:49.658][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:49.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:49.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:49.660][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:49.661][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.662][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:49.663][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:49.664][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:49.665][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:49.667][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:49.668][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.673][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[2025-01-02 20:19:49.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.713][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[2025-01-02 20:19:49.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.717][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[2025-01-02 20:19:49.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.735][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[2025-01-02 20:19:49.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.745][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-02 20:19:49.747][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-02 20:19:49.749][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-02 20:19:49.750][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-02 20:19:49.752][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-02 20:19:49.753][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-02 20:19:49.754][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-02 20:19:49.756][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-02 20:19:49.757][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-02 20:19:49.759][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-02 20:19:49.760][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-02 20:19:49.762][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-02 20:19:49.763][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-02 20:19:49.764][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-02 20:19:49.766][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-02 20:19:49.767][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-02 20:19:49.769][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-02 20:19:49.770][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-02 20:19:49.771][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-02 20:19:49.773][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-02 20:19:49.774][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-02 20:19:49.776][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-02 20:19:49.777][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-02 20:19:49.778][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-02 20:19:49.780][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-02 20:19:49.781][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-02 20:19:49.789][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-02 20:19:49.791][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-02 20:19:49.792][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-02 20:19:49.794][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-02 20:19:49.795][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-02 20:19:49.796][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-02 20:19:49.798][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-02 20:19:49.799][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-02 20:19:49.800][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-02 20:19:49.802][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-02 20:19:49.803][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-02 20:19:49.804][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-02 20:19:49.806][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-02 20:19:49.807][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-02 20:19:49.808][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-02 20:19:49.810][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-02 20:19:49.811][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-02 20:19:49.812][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-02 20:19:49.814][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-02 20:19:49.815][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-02 20:19:49.817][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-02 20:19:49.818][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-02 20:19:49.819][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-02 20:19:49.821][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-02 20:19:49.822][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-02 20:19:49.823][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-02 20:19:49.825][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-02 20:19:49.827][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-02 20:19:49.828][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-02 20:19:49.830][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-02 20:19:49.831][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-02 20:19:49.833][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-02 20:19:49.834][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-02 20:19:49.835][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-02 20:19:49.837][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-02 20:19:49.838][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-02 20:19:49.839][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-02 20:19:49.841][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-02 20:19:49.842][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-02 20:19:49.844][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-02 20:19:49.845][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-02 20:19:49.846][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-02 20:19:49.848][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-02 20:19:49.849][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-02 20:19:49.850][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-02 20:19:49.852][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-02 20:19:49.853][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-02 20:19:49.855][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-02 20:19:49.856][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-02 20:19:49.858][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-02 20:19:49.859][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-02 20:19:49.860][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-02 20:19:49.862][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-02 20:19:49.863][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-02 20:19:49.864][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-02 20:19:49.866][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-02 20:19:49.867][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-02 20:19:49.869][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-02 20:19:49.870][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-02 20:19:49.871][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:49.872][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.874][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.875][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[2025-01-02 20:19:49.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.891][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[2025-01-02 20:19:49.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.950][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[2025-01-02 20:19:49.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.963][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[2025-01-02 20:19:49.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.981][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[2025-01-02 20:19:49.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:49.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:49.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:49.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:49.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:49.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:49.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:49.995][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-02 20:19:49.997][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-02 20:19:49.999][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:50.000][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-02 20:19:50.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:50.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:50.003][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:50.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:50.004][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:50.005][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-02 20:19:50.006][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-02 20:19:50.007][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:50.008][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:50.009][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-02 20:19:50.010][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-02 20:19:50.011][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-02 20:19:50.013][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:50.014][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:50.014][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:50.014][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:50.015][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-02 20:19:50.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:50.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:50.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:50.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:50.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:50.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:50.021][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:50.021][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-02 20:19:50.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:50.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:50.024][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:50.025][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-02 20:19:50.025][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-02 20:19:50.026][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-02 20:19:50.028][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-02 20:19:50.030][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-02 20:19:50.031][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-02 20:19:50.033][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-02 20:19:50.034][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-02 20:19:50.038][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-02 20:19:50.039][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-02 20:19:50.040][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-02 20:19:50.042][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-02 20:19:50.043][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-02 20:19:50.044][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-02 20:19:50.045][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-02 20:19:50.046][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-02 20:19:50.048][biodb::testThat]
biodb.INFO [2025-01-02 20:19:50.048][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-01-02 20:19:50.049][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:50.050][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:50.054][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-02 20:19:50.058][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:50.059][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:50.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-01-02 20:19:50.392][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-01-02 20:19:50.887][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:50.890][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-01-02 20:19:50.893][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-01-02 20:19:50.897][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[2025-01-02 20:19:50.900][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:50.901][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:50.903][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-02 20:19:51.243][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:51.595][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:51.599][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-01-02 20:19:51.605][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-01-02 20:19:51.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:51.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:51.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:51.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:51.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:51.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:51.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:51.625][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:51.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:51.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:51.632][private$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[2025-01-02 20:19:51.975][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[2025-01-02 20:19:52.317][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:52.322][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-01-02 20:19:52.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-01-02 20:19:52.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:52.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:52.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:52.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:52.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:52.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:52.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:52.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:52.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:52.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:52.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:52.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:52.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:52.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:52.621][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[2025-01-02 20:19:52.624][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:52.626][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-01-02 20:19:52.627][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:52.628][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-01-02 20:19:52.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:52.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:52.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:52.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:52.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:52.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:52.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:52.641][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[2025-01-02 20:19:52.644][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:52.645][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-01-02 20:19:52.646][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:52.648][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-01-02 20:19:52.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:52.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:52.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:52.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:52.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:52.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:52.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:52.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:52.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:52.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:52.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:52.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:52.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:52.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:52.677][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[2025-01-02 20:19:52.682][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:52.683][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-01-02 20:19:52.684][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:52.686][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-01-02 20:19:52.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:52.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:52.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:52.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:52.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:52.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:52.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:52.700][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[2025-01-02 20:19:52.703][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:52.705][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-01-02 20:19:52.706][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:52.707][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-01-02 20:19:52.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:52.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:52.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:52.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:52.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:52.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:52.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:52.722][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[2025-01-02 20:19:52.725][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:52.726][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:52.728][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-02 20:19:53.079][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:53.421][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:53.423][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-01-02 20:19:53.427][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-01-02 20:19:53.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:53.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:53.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:53.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:53.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:53.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:53.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-02 20:19:53.445][biodb::testThat]
biodb.INFO [2025-01-02 20:19:53.446][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-01-02 20:19:53.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:53.447][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:53.451][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:53.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:53.455][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:53.457][private$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[2025-01-02 20:19:53.794][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[2025-01-02 20:19:54.138][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:54.141][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-01-02 20:19:54.148][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-01-02 20:19:54.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:54.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:54.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:54.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:54.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:54.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.194][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[2025-01-02 20:19:54.200][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:54.201][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:54.204][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-02 20:19:54.544][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-02 20:19:54.883][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:54.885][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-01-02 20:19:54.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-01-02 20:19:54.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:54.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:54.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:54.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:54.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:54.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-02 20:19:54.906][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-02 20:19:54.907][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-02 20:19:54.908][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-02 20:19:54.922][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-02 20:19:54.923][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:54.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:54.924][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:54.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:54.926][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-02 20:19:54.930][biodb::testContext]
biodb.INFO [2025-01-02 20:19:54.931][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-02 20:19:54.932][biodb::testContext] Test context - Test web services
biodb.INFO [2025-01-02 20:19:54.933][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-02 20:19:54.934][biodb::testContext]
biodb.INFO [2025-01-02 20:19:54.936][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-02 20:19:54.937][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-02 20:19:54.941][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:54.942][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-02 20:19:54.943][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-02 20:19:54.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.946][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-02 20:19:54.947][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-02 20:19:54.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.951][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-02 20:19:54.952][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-02 20:19:54.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.955][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-02 20:19:54.956][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-02 20:19:54.957][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-02 20:19:54.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.960][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-02 20:19:54.961][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-02 20:19:54.962][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-02 20:19:54.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.965][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-02 20:19:54.966][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-02 20:19:54.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.970][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-02 20:19:54.971][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-02 20:19:54.972][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-02 20:19:54.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.975][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-02 20:19:54.976][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-02 20:19:54.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.979][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-02 20:19:54.980][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-02 20:19:54.981][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-02 20:19:54.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.984][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-02 20:19:54.985][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-02 20:19:54.986][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-02 20:19:54.987][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-02 20:19:54.988][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-02 20:19:54.989][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-02 20:19:54.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.992][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-02 20:19:54.993][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-02 20:19:54.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:54.996][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-02 20:19:54.997][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-02 20:19:54.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:54.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:54.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.000][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-02 20:19:55.001][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-02 20:19:55.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.005][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-02 20:19:55.006][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-02 20:19:55.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.009][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-02 20:19:55.010][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-02 20:19:55.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.014][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-02 20:19:55.015][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-02 20:19:55.018][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-02 20:19:55.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.022][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-02 20:19:55.023][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-02 20:19:55.024][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-02 20:19:55.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.027][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.DEBUG[2025-01-02 20:19:55.028][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-02 20:19:55.030][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.031][self$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[2025-01-02 20:19:55.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:55.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.036][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.037][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.038][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-02 20:19:55.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:55.040][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.041][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-02 20:19:55.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:55.043][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.044][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.045][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:55.045][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:55.045][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:55.045][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-02 20:19:55.045][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-02 20:19:55.046][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:55.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.049][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:55.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.052][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.053][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.054][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:55.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:55.066][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.067][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.068][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-02 20:19:55.070][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.071][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-02 20:19:55.072][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.073][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:55.074][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.075][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.076][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.076][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.077][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-02 20:19:55.078][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:55.079][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.080][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-02 20:19:55.081][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:55.082][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.083][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.084][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:55.084][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:55.084][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:55.084][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-02 20:19:55.084][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-02 20:19:55.085][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:55.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.088][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:55.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.090][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.091][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.092][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:55.093][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:55.094][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.095][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.096][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-02 20:19:55.097][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.098][self$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[2025-01-02 20:19:55.099][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.100][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:55.101][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.102][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.103][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.104][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.105][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-02 20:19:55.106][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:55.107][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.108][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-02 20:19:55.109][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:55.109][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.110][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.111][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.112][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:55.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:55.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.117][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.118][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:55.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:55.121][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.122][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.123][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-02 20:19:55.125][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.126][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-02 20:19:55.127][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.128][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:55.128][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.129][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.130][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.131][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.132][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-02 20:19:55.133][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:55.134][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.135][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-02 20:19:55.136][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:55.137][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.138][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.139][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.140][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:55.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.143][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:55.144][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.145][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.146][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.147][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:55.148][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:55.149][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.150][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:55.151][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:55.152][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.166][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[2025-01-02 20:19:55.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.171][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.DEBUG[2025-01-02 20:19:55.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.179][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[2025-01-02 20:19:55.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.228][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[2025-01-02 20:19:55.229][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-02 20:19:55.236][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-02 20:19:55.237][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-02 20:19:55.238][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-02 20:19:55.240][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-02 20:19:55.241][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-02 20:19:55.242][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-02 20:19:55.244][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-02 20:19:55.245][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-02 20:19:55.246][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-02 20:19:55.248][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-02 20:19:55.249][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-02 20:19:55.250][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-02 20:19:55.252][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-02 20:19:55.253][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-02 20:19:55.254][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-02 20:19:55.256][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-02 20:19:55.257][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-02 20:19:55.258][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-02 20:19:55.260][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-02 20:19:55.261][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-02 20:19:55.262][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-02 20:19:55.264][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-02 20:19:55.265][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-02 20:19:55.266][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-02 20:19:55.268][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-02 20:19:55.269][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-02 20:19:55.270][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-02 20:19:55.272][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-02 20:19:55.274][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-02 20:19:55.276][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-02 20:19:55.278][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-02 20:19:55.280][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-02 20:19:55.282][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-02 20:19:55.284][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-02 20:19:55.285][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-02 20:19:55.287][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-02 20:19:55.289][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-02 20:19:55.291][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-02 20:19:55.293][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-02 20:19:55.295][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-02 20:19:55.297][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-02 20:19:55.299][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-02 20:19:55.300][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-02 20:19:55.302][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-02 20:19:55.304][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-02 20:19:55.306][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-02 20:19:55.308][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-02 20:19:55.310][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-02 20:19:55.312][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-02 20:19:55.314][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-02 20:19:55.316][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-02 20:19:55.318][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-02 20:19:55.319][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-02 20:19:55.321][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-02 20:19:55.323][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-02 20:19:55.325][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-02 20:19:55.327][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-02 20:19:55.329][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-02 20:19:55.331][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-02 20:19:55.333][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-02 20:19:55.335][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-02 20:19:55.337][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-02 20:19:55.339][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-02 20:19:55.341][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-02 20:19:55.342][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-02 20:19:55.344][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-02 20:19:55.346][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-02 20:19:55.348][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-02 20:19:55.350][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-02 20:19:55.352][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-02 20:19:55.354][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-02 20:19:55.356][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-02 20:19:55.358][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-02 20:19:55.360][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-02 20:19:55.362][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-02 20:19:55.363][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-02 20:19:55.365][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-02 20:19:55.367][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-02 20:19:55.369][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-02 20:19:55.371][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-02 20:19:55.373][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-02 20:19:55.375][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-02 20:19:55.377][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-02 20:19:55.379][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-02 20:19:55.380][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:55.382][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.384][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.385][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[2025-01-02 20:19:55.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.394][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[2025-01-02 20:19:55.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.400][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[2025-01-02 20:19:55.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.442][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[2025-01-02 20:19:55.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.465][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[2025-01-02 20:19:55.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:55.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:55.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:55.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:55.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:55.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:55.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:55.497][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-02 20:19:55.498][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-02 20:19:55.500][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.501][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.502][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.503][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:55.504][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.505][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.506][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.507][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-02 20:19:55.507][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-02 20:19:55.508][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:55.509][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.510][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-02 20:19:55.511][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-02 20:19:55.512][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-02 20:19:55.513][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:55.514][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:55.514][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:55.514][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:55.515][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-02 20:19:55.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.518][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:55.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:55.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:55.521][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:55.522][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:55.522][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-02 20:19:55.523][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:55.524][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:55.525][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:55.526][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-02 20:19:55.526][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-02 20:19:55.527][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-02 20:19:55.528][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-02 20:19:55.530][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-02 20:19:55.532][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-02 20:19:55.533][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-02 20:19:55.535][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-02 20:19:55.538][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-02 20:19:55.539][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-02 20:19:55.540][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-02 20:19:55.541][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-02 20:19:55.543][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-02 20:19:55.544][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-02 20:19:55.545][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-02 20:19:55.546][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-02 20:19:55.547][biodb::testThat]
biodb.INFO [2025-01-02 20:19:55.548][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-01-02 20:19:55.549][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:55.550][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:55.553][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-02 20:19:55.557][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:55.558][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-02 20:19:55.559][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:55.561][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-02 20:19:55.565][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:55.568][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:55.569][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:55.570][private$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[2025-01-02 20:19:55.914][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[2025-01-02 20:19:56.252][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:56.255][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-01-02 20:19:56.259][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-01-02 20:19:56.268][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-02 20:19:56.269][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-02 20:19:56.270][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-02 20:19:56.271][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-02 20:19:56.272][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.273][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.275][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.276][FUN] Functions in observer BiodbConfig: [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 [2025-01-02 20:19:56.279][biodb::testContext]
biodb.INFO [2025-01-02 20:19:56.280][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-02 20:19:56.281][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-01-02 20:19:56.282][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-02 20:19:56.283][biodb::testContext]
biodb.INFO [2025-01-02 20:19:56.285][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-02 20:19:56.287][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-02 20:19:56.291][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:56.292][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-02 20:19:56.293][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-02 20:19:56.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.307][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-02 20:19:56.308][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-02 20:19:56.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.312][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-02 20:19:56.313][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-02 20:19:56.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.316][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-02 20:19:56.317][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-02 20:19:56.318][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-02 20:19:56.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.322][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-02 20:19:56.323][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-02 20:19:56.324][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-02 20:19:56.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.327][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-02 20:19:56.328][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-02 20:19:56.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.331][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[2025-01-02 20:19:56.332][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-02 20:19:56.333][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-02 20:19:56.334][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-02 20:19:56.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.338][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-02 20:19:56.339][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-02 20:19:56.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.342][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-02 20:19:56.343][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-02 20:19:56.344][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-02 20:19:56.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.347][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-02 20:19:56.348][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-02 20:19:56.349][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-02 20:19:56.350][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-02 20:19:56.351][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-02 20:19:56.352][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-02 20:19:56.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.355][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-02 20:19:56.356][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-02 20:19:56.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.360][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-02 20:19:56.360][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-02 20:19:56.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.364][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-02 20:19:56.365][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-02 20:19:56.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.368][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-02 20:19:56.369][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-02 20:19:56.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.372][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-02 20:19:56.373][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-02 20:19:56.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.377][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-02 20:19:56.378][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-02 20:19:56.382][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-02 20:19:56.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.385][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-02 20:19:56.386][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-02 20:19:56.387][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-02 20:19:56.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.390][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-02 20:19:56.392][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.393][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-02 20:19:56.394][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.395][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:56.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.397][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.398][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.399][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.399][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-02 20:19:56.400][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:56.401][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.402][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-02 20:19:56.403][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:56.404][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.405][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.406][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:56.406][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:56.406][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:56.406][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-02 20:19:56.406][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-02 20:19:56.407][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:56.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.409][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:56.410][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.412][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.413][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.414][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:56.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:56.415][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.416][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.417][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-02 20:19:56.419][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.420][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-02 20:19:56.421][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.422][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:56.423][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.424][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.425][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.426][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.427][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-02 20:19:56.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:56.429][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.430][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-02 20:19:56.431][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:56.432][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.434][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:56.434][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:56.434][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:56.434][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-02 20:19:56.434][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-02 20:19:56.435][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:56.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.438][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:56.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.440][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.441][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.442][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:56.443][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:56.444][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.445][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.446][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-02 20:19:56.448][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.449][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-02 20:19:56.450][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.451][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:56.452][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.453][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.454][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.455][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.456][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-02 20:19:56.457][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:56.458][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.458][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-02 20:19:56.459][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:56.460][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.461][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.462][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.463][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:56.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.466][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:56.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.474][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.475][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.476][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:56.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:56.477][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.478][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.480][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-02 20:19:56.481][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.482][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-02 20:19:56.483][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.484][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:56.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.487][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.489][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-02 20:19:56.490][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:56.491][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.492][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-02 20:19:56.493][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:56.494][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.495][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.496][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.497][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-02 20:19:56.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.499][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:56.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.503][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:56.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:56.506][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.507][self$setPropertyValue]
biodb.DEBUG[2025-01-02 20:19:56.508][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:56.509][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.510][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[2025-01-02 20:19:56.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.527][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[2025-01-02 20:19:56.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.535][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[2025-01-02 20:19:56.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.539][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[2025-01-02 20:19:56.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.551][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[2025-01-02 20:19:56.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.559][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[2025-01-02 20:19:56.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.563][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[2025-01-02 20:19:56.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.580][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[2025-01-02 20:19:56.581][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-02 20:19:56.582][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-02 20:19:56.583][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-02 20:19:56.585][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-02 20:19:56.586][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-02 20:19:56.587][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-02 20:19:56.589][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-02 20:19:56.590][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-02 20:19:56.591][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-02 20:19:56.593][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-02 20:19:56.594][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-02 20:19:56.595][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-02 20:19:56.597][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-02 20:19:56.598][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-02 20:19:56.600][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-02 20:19:56.601][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-02 20:19:56.602][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-02 20:19:56.603][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-02 20:19:56.605][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-02 20:19:56.606][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-02 20:19:56.608][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-02 20:19:56.609][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-02 20:19:56.610][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-02 20:19:56.612][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-02 20:19:56.613][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-02 20:19:56.614][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-02 20:19:56.615][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-02 20:19:56.617][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-02 20:19:56.618][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-02 20:19:56.619][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-02 20:19:56.621][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-02 20:19:56.622][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-02 20:19:56.623][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-02 20:19:56.625][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-02 20:19:56.626][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-02 20:19:56.627][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-02 20:19:56.628][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-02 20:19:56.635][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-02 20:19:56.637][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-02 20:19:56.638][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-02 20:19:56.639][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-02 20:19:56.641][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-02 20:19:56.642][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-02 20:19:56.643][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-02 20:19:56.645][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-02 20:19:56.646][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-02 20:19:56.647][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-02 20:19:56.648][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-02 20:19:56.650][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-02 20:19:56.651][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-02 20:19:56.652][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-02 20:19:56.654][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-02 20:19:56.655][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-02 20:19:56.656][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-02 20:19:56.658][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-02 20:19:56.659][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-02 20:19:56.660][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-02 20:19:56.662][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-02 20:19:56.663][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-02 20:19:56.664][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-02 20:19:56.666][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-02 20:19:56.667][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-02 20:19:56.668][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-02 20:19:56.669][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-02 20:19:56.671][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-02 20:19:56.672][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-02 20:19:56.673][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-02 20:19:56.674][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-02 20:19:56.676][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-02 20:19:56.677][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-02 20:19:56.678][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-02 20:19:56.679][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-02 20:19:56.681][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-02 20:19:56.682][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-02 20:19:56.683][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-02 20:19:56.684][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-02 20:19:56.686][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-02 20:19:56.687][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-02 20:19:56.688][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-02 20:19:56.690][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-02 20:19:56.691][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-02 20:19:56.692][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-02 20:19:56.693][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-02 20:19:56.695][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-02 20:19:56.696][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-02 20:19:56.697][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-02 20:19:56.698][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.700][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.723][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[2025-01-02 20:19:56.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.729][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[2025-01-02 20:19:56.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.735][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[2025-01-02 20:19:56.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.771][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[2025-01-02 20:19:56.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.777][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[2025-01-02 20:19:56.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.783][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[2025-01-02 20:19:56.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-02 20:19:56.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.806][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[2025-01-02 20:19:56.808][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-02 20:19:56.809][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-02 20:19:56.811][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.812][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.813][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.814][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-02 20:19:56.815][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.816][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.817][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.818][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-02 20:19:56.819][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-02 20:19:56.819][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-02 20:19:56.820][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.821][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-02 20:19:56.822][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-02 20:19:56.823][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-02 20:19:56.824][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-02 20:19:56.825][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-02 20:19:56.825][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-02 20:19:56.825][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-02 20:19:56.826][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-02 20:19:56.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.829][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-02 20:19:56.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-02 20:19:56.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-02 20:19:56.832][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-02 20:19:56.832][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:56.832][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-02 20:19:56.833][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-02 20:19:56.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-02 20:19:56.835][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-02 20:19:56.836][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-02 20:19:56.836][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-02 20:19:56.837][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-02 20:19:56.839][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-02 20:19:56.841][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-02 20:19:56.842][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-02 20:19:56.844][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-02 20:19:56.845][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-02 20:19:56.848][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-02 20:19:56.849][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-02 20:19:56.850][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-02 20:19:56.852][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-02 20:19:56.853][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-02 20:19:56.854][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-02 20:19:56.855][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-02 20:19:56.856][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-02 20:19:56.858][biodb::testThat]
biodb.INFO [2025-01-02 20:19:56.859][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-01-02 20:19:56.859][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-02 20:19:56.860][biodb::testThat]
biodb.DEBUG[2025-01-02 20:19:56.863][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-02 20:19:56.867][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:56.868][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-02 20:19:56.870][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:56.871][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-02 20:19:56.874][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-02 20:19:56.877][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-02 20:19:56.879][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-01-02 20:19:56.880][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-02 20:19:56.881][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-01-02 20:19:56.886][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-01-02 20:19:56.886][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-02 20:19:56.888][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-01-02 20:19:56.889][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-02 20:19:56.890][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-02 20:19:56.891][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-02 20:19:56.892][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-02 20:19:56.893][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-02 20:19:56.894][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-02 20:19:56.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:56.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:56.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:56.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:56.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:56.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:56.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-02 20:19:56.907][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-01-02 20:19:56.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-02 20:19:56.910][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-02 20:19:56.912][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-01-02 20:19:57.260][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-01-02 20:19:58.278][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-02 20:19:58.282][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-01-02 20:19:58.287][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-01-02 20:19:58.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-01-02 20:19:58.294][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-02 20:19:58.295][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-02 20:19:58.297][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-02 20:19:58.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-02 20:19:58.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:58.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:58.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:58.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:58.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:58.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-02 20:19:58.319][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:58.320][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:58.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.322][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:58.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:58.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.328][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:58.329][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:58.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.331][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.332][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-02 20:19:58.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-02 20:19:58.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.336][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:58.337][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:58.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.339][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-02 20:19:58.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-02 20:19:58.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.345][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-02 20:19:58.346][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-02 20:19:58.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.355][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.361][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-02 20:19:58.362][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-02 20:19:58.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.364][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.366][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:58.367][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:58.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.368][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.370][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:58.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-02 20:19:58.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.374][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:58.375][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:58.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.377][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.378][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-02 20:19:58.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-02 20:19:58.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.382][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:58.383][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:58.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.384][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:58.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-02 20:19:58.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.390][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:58.391][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:58.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.392][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-02 20:19:58.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-02 20:19:58.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.398][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:58.399][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:58.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.401][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.402][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-02 20:19:58.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-02 20:19:58.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.406][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:58.407][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:58.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.409][ef$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.410][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-02 20:19:58.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-02 20:19:58.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:58.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:58.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:58.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:58.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:58.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:58.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-02 20:19:58.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-02 20:19:58.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:58.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:58.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:58.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:58.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:58.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:58.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:58.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:58.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:58.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:58.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-02 20:19:58.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-02 20:19:58.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-02 20:19:58.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-02 20:19:58.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-02 20:19:58.452][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-01-02 20:19:58.455][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-02 20:19:58.456][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-02 20:19:58.457][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-02 20:19:58.458][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-02 20:19:58.459][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-02 20:19:58.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-02 20:19:58.461][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-02 20:19:58.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-02 20:19:58.462][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-02 20:19:58.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 22.628   0.843  54.860

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	0.903	0.073	2.055
ChebiEntry	0.149	0.003	0.151